Mental Burdocks

Probiotic anti-depressants?

2011-08-30T07:56:00.003-04:00

In what might be the the quintessential post for a blog titled Mental Burdocks, I wanted to point out a recent microbiome study that suggests there is a potential for gut bacteria to have impacts on the mind and mood. Researchers found that mice fed widely available probiotic Lactobacillus bacteria showed fewer signs of stress and a greater inclination towards exploration.

This would seem to indicate another level of depth to the old adage 'you are what you eat'.

UPDATE 8/31: Another new study looked at the impact of diet on the viral communities in the gut. The study found that while individual communities varied substantially and remained relatively stable over time, the communities of individuals on similar diets showed convergence.

UPDATE 9/1: By pure coincidence, the seminar at work today was "Inside story: the role of gut microbes in nutrition and drug metabolism", by Peter Turnbaugh, PhD. Peter is from the FAS Center for Systems Biology at Harvard, where their research "involves the development and application of computational and experimental methods for the analysis of community structure, gene content, and function of complex microbial communities." His talk generated lots of discussion, and left me wondering whether anyone has looked at the well-studied impact of caloric restriction on longevity from the perspective of the microbiome - Google doesn't turn up much.

UPDATE 9/2: A paper published in Science yesterday surveys the enterotypes in the human gut and finds they are linked to dietary habits (high protein/saturated fat vs high carbs, etc). It also found that while some shift occurs in the span of hours following a diet change, long term dietary changes are required to change an individual's gut enterotype conclusively.

UPDATE 9/15: Peter got back to me on my question, he reports there are a couple of studies that are related to longevity and the microbiome, but nothing looking directly at whether "specific microbial consortia impact longevity." Also, researchers in Europe have opened my.microbes to the public, in case you are looking to participate in a study and are willing to spend ~$2100 to have your gut bacteria sequenced.

Aging as a Disease

2011-07-07T10:00:00.002-04:00

Source: Reuters

There's a reasonably fresh story running around the wires from Aubrey de Grey, a fairly well-known gerontologist, which reminds me of some of the pieces of the Ray Kurzweil keynote I saw at SC a number of years ago. Ray showed one of his many exponential progress curves that indicated human lifespan was getting close to a point were for every year we lived, we would gain more than a year in average lifespan. Aubrey's claim is that "we have a 50/50 chance of bringing aging under what I'd call a decisive level of medical control within the next 25 years or so" and that "the first person who will live to see their 150th birthday has already been born". Perhaps most mind-bending is his claim that within 20 years of the first person to turn 150, someone will be born who will live to 1000.

HHMI, Max Planck and Wellcome Trust Announce Plans for new Open Access Journal

2011-06-27T10:49:00.000-04:00

The top-tier organizations in the biomedical and life sciences have announced plans to launch an open access journal in the summer of 2012. The plans are the result of a 2010 workshop at HHMI's Janelia Farm, where participants concluded there is a new for a new publishing model. There are several key themes for the new effort - more efficient, responsive publication of research, editorial participation by actively practicing scientists, a digital-only presence, and a move away from requests for modifications or follow-on studies that extend the publication process.

There is hope that this kind of approach to sharing of research findings can help speed the pace of discovery.

Next-Gen Sequencing in the Nic of Time

2011-03-02T14:40:00.005-05:00

The Milwaukee-Wisconsin Journal Sentinel has an in-depth write-up on Nic Volker, the young boy with a incredible story of disease and recovery based in next-generation sequencing. George Church, pioneering the Harvard/MIT geneticist, briefly cited this [at that time anonymous] case in his evening keynote back at the Harvard BioMed HPC Summit in October 2010.

Even without the cutting edge science that finally identified the mutation that was the basis for Nic's disease, it's an incredible story - the young boy survived just about every horror you can imagine - multiple bouts with sepsis, chemo, hundreds of surgeries, encephalitis.

The feature goes on to provide an update that suggests that Nic's case may be the leading edge of a wave moving across genetic medicine. While sequencing is a long ways from a miracle cure for huge percentages of diseases, the victories, few as they are, are exciting.

UPDATE 6/28/11 - Another similar story just came through of California twins with a rare condition that wasn't responding to treatment until their genomes as well as the genomes of their older brother, parents and grandparents were sequenced. It's an incredible story, and while this kind of approach is currently beyond the reach of many (~$10K per genome), the cost is falling at roughly 5X per year, putting into reach of routine medicine within several years.

The Original Leatherman?

2011-01-25T08:33:00.000-05:00

Slightly off-topic, but I'm a big fan of fixing things, and that often requires a handy tool. I carried a Swiss Army knife for many years, and then Leathermans once they came on the scene. It's remarkable how similar an 1,800 old year Roman tool is to those of today. The other must-have is a small waterproof LED flashlight, but that's a topic for another post.

50 Ideas to Change Science: MPD

2010-10-11T12:19:00.002-04:00

Source: MPD

Jackson's own Mouse Phenome Database has made NewScientist's list of 50 Ideas to Change Science. From the article:

"If we want truly to understand the living world, the genome won't do. We need to get to grips with the "phenome": the sum total of all traits, from genes to behaviour, that make up a living thing. [...] That complexity perhaps explains why there is as yet no "human phenome project", though such a thing was first mooted in 2003. But smaller-scale projects such as the Mouse Phenome Database are now springing up. From personalised medicine to our understanding of evolution, science will be the beneficiary."

MPD enables searches based on 2208 physiological and behavioral data, as well as strain, projects, protocols, interventions (ie drugs, chemicals, diets, etc), testing apparatus, and other criteria, and is being utilized by close to 7000 different visitors per month.

Cars That Drive Themselves Pass the 1000 Mile Mark

2010-10-11T09:09:00.002-04:00

Source: NY Times

Not a new story per se, but interesting in that Google has been testing autonomous cars in traffic, and they've gone 1000+ miles without human intervention (and 140,000 miles with only occasional intervention). The NY Times story suggests that autonomous vehicles have the potential to transform society as dramatically as the Internet. It would certainly fix the texting while driving issue once and for all. The programming is sophisticated enough at this point to have styles of driving ranging from cautious to aggressive. It's fascinating that Google is obviously putting non-trivial resources into this research... makes you wonder what else they are working on.

UPDATE: Deepak Singh has an interesting post on this kind of speculative research.

The Cancer Breathalzyer? On Your Cellphone?

2010-09-01T08:36:00.001-04:00

A friend forward a link to a very interesting study in the British Journal of Cancer that shows the potential for developing a breath test that can identify volatile organic compounds associated with four different kinds of cancer (breast, colon, lung, and prostate). Peng et al utilized a custom nanosensor "array of cross-reactive sensors based on organically functionalised gold nanoparticles." It would be fascinating if this kind of array technology could be combined with the Xprize initiative to create an artificially intelligent physician on a smartphone.

Next-Gen HDR Photography: Down to the Pixel

2010-08-03T10:33:00.000-04:00

I've been mucking with high-dynamic range photography for a year or so, and ever since I was introduced to the technology, it seemed clear to me that it was only a matter of time before the ability to adjust for differing light intensities moved from the entire sensor (the current HDR process) to individual sensor pixels. Canon has recently submitted a patent application for just such an approach... while we're still years away from such a device, it's interesting to see movement in that direction.

Multitouch Table Taken to the Next Level

2010-08-03T08:34:00.002-04:00

Very interesting demo of a multitouch interactive table that includes magnetically controlled widgets. While there have been tables that allow physical widgets such as knobs to provide input to the table, this setup gives the table the ability to control physical objects. While fascinating to watch, I'm having some trouble thinking up a good application for this.

The Microbiome: You Are Not Alone In There

2010-07-30T16:44:00.004-04:00

In the age-old dispute of nature vs nurture, the study of the microbiome has a lot to offer to the nurture crowd. As noted in Science, a recent paper in Nature looked at the genomes of the viruses (viromes) living in the digestive tracts of human twins, and found a remarkable lack of similarity between individuals, no more so than between any two random individuals. This is somewhat surprising because earlier work looking at the bacterial communities in the gut shows much greater similarities between individuals who are related.

It feels like we may be on the cusp of a change in how we think about ourselves, at least with respect to our health. As we improve our ability to understand the complex relationships among the huge number of microbes we have for roommates, and how our external environment and diet impacts these communities, it seems likely that we will uncover major implications for our health and wellness. The spiritual world has long nurtured the idea of a deep and powerful connection between ourselves and the world around us, but perhaps that connection is much closer and personal than we ever thought. As noted in an NY Times editorial related to this paper:

"We are not just the expression of an individual human genome. We are, as Dr. Gordon writes, “a genetic landscape,” a collective of genomes of hundreds of different species all working together — in ways that leave our minds mysteriously free to focus on getting our bodies to the office and wondering what’s for lunch."

Costs of Solar vs Nuclear Power: Fight!

2010-07-30T16:24:00.002-04:00

Very interesting news from a study from Duke University looking at the costs trends of solar and nuclear energy, at least in North Carolina. As one would expect, the cost of solar has been falling, but what's surprising is that the cost of nuclear is climbing at the rate they indicate. This is attributed to the "nuclear renaissance" and the associated redesign of the facilities, for which projections continue to climb as the planning gets into the specifics. Based on this work, it would seem unlikely that many more nuclear plants will be constructed.

The bad news for those of us at higher latitudes is that the solar photovoltaic potential is considerably lower here. But then we've got quite few wind power initiatives in the works. I'd love to see the wind power costs overlaid on this chart.

8/3/10 - UPDATE: Stanford researchers announce a new method for harvesting both light and heat energy from the sun, potentially doubling power output. This could be the nail in the coffin of nuclear if it pans out.

The Mathematics of Genome Sequencing

2010-07-07T06:12:00.001-04:00

The mathematics magazine Plus has an interesting, accessible article that looks at the mathematics and programming approaches to genome sequencing. My suspicion is that most people assume sequencing is perfectly accurate, but once you get into the weeds you realize it's messy in there.

HDR and Microscopy

2010-06-15T13:29:00.004-04:00

I've been having a blast over the last year or so getting back into photography after about a 3 decade lapse (and major advances in technology). The thing that really got me excited was something called high dynamic range or HDR photography.

One of the basic rules in photography has been that you should have the shot's light source (in particular the sun) at your back, otherwise your exposure might be funky. HDR involves taking multiple images at different exposures of the same subject so that you can get the very bright and very dark areas at appropriate exposures. The human eye and brain have an amazing ability to handle these tremendous differences in a particular view, and to my eye HDR gives the photographer some tools to get closer to what we perceive (and to also take some artistic license with the images). I really enjoy the ability to shoot directly into the sun.

Even more interesting is the potential to apply this technique to scientific imaging. We've had some discussions about improving surgery images, and I spent some time brainstorming with our microscopy folks, one of whom forwarded along this paper which covers very nicely how HDR can enhance bright-field microscopy. Interestingly enough, they also use the same HDR software I've been working with (Photomatix Pro). It's really exciting to see someone tackling this.

Images C and D are HDR.
Image: Joerg Piper, Bad Bertrich, Germany, 2010

New Study Shows Genomic Counseling Results in Lifestyle Changes

2010-06-09T05:26:00.003-04:00

While there has been lot of attention paid to the incredible pace of advancement in sequencing technology, there is growing discussion around the medical value of the data. Knowing that you carry a certain allele for disease risk may be interesting, but what do you do with that data? Do you change lifestyle? Do you begin a proactive course of medication? What is appropriate and who helps you understand the data and the potentially difficult choices it creates? There has even been concern that individuals, upon finding out they are at higher risk for a disease, would "give up", resulting in decreased quality of health.

A recent study by the Coriell Institute finds that:

"People who find out they have high genetic risk for cardiovascular disease are more likely to change their diet and exercise patterns than are those who learn they have a high risk from family history, according to preliminary research."

It's interesting to see that genetic testing appears to have the potential to be more motivating for patients than traditional sources of similar information, though it's hard to know whether it's a function of the novelty of the data or something more lasting. It's also important to note that there appears to have been high quality counseling associated with this study, which is widely seen as a critical to appropriate use of genetic data.

A New Culture of Scientific Communication

2010-06-03T08:34:00.005-04:00

It's great to see Josh Sommer's excellent talk at the Sage Congress getting more attention. Josh is a 22 year-old college drop-out who was diagnosed with a very rare brain tumor called chordoma as a freshman at Duke. When he discovered the average life expectancy for this disease is seven years and only 20-30% of the patients are cured, he immediately began reading the research. He was disturbed to discover how little research was going on related to chordoma and began working in the lab of a Duke researcher, but realized that progress was still way too slow. He then began to identify the things that were slowing down the speed of the research, and eventually founded the Chordoma Foundation in 2007 to begin attacking these barriers.

The first barrier they decided to tackle was the relatively limited flow of information between chrodoma researchers. As the foundation led workshops and brought researchers together, they saw substantial increase in the number of questions around the disease being answered, and eventually built a research roadmap. He makes a compelling case for the need to change from a publishing model established 400 years ago that is no longer appropriate for the rapid pace of technology to an open access model that changes the culture for data and information sharing across the scientific community.

Grow New Teeth

2010-05-29T07:16:00.001-04:00

Columbia researchers have developed a method of applying stem cells to scaffolding infused with growth hormone to grow teeth in a little as nine weeks in an animal model. A major move forward here has been to growth the teeth in situ instead of in the laboratory, which improves their final shape.

One Mutation for Every Three Cigarettes

2010-05-27T08:51:00.001-04:00

If you need more evidence that cigarettes are tremendously unhealthy, Genentech and Complete Genomics have published the full genome sequence of a primary lung tumor from a heavy smoker in a Nature paper. The tumor had as many as 50,000 mutated genes, from which they calculated that one mutation occurred for every three cigarettes smoked.

Very Impressive Quadruped Robot

2010-05-26T08:56:00.003-04:00

Fascinating video of a quadrupedal robot from USC's Computational Learning and Motor Control Lab that can handle novel, challenging terrain, and can learn how to make good foothold choices.

A Switch to Turn on Youthful Memory

2010-05-20T18:27:00.001-04:00

A very interesting study found that acetylation of chromatin in DNA resulted in expression changes that gave older mice the learning and memory performance of a youngster. What a great example of how critical epigenetics is to understanding the big picture, just knowing the genes isn't enough, you have to understand how they are (or are not) expressed.

New Blog Techtilis Focusing on Bio-IT Infrastructure Planning

2010-05-20T18:20:00.001-04:00

I've started a new blog Techtilis to focus on the issues and challenges of planning IT infrastructure in support of genetics research. Mental Burdocks will continue on as a more general blog of science and technology items.

Matthew Trunnell on Data Management Challenges at The Broad

2010-04-22T10:15:00.003-04:00

Matthew Trunnell, Acting Director, Advanced IT, Broad Institute gave a talk in Track 1 Infrastructure - Hardware at Bio-IT World on Adjusting to the New Scale of Research Data Management. The Broad has been struggling with the PBs of data associated with their massive sequencing facilities for four years (he noted he ordered 1.1 PB of new storage last week), and is now encountering the issues associated with managing massive data collections that have challenge the physics and space engineering communities (among others) for the last 10-20 years.

He noted that as data grow very large, if it's not well managed you start to spend substantial amounts of time looking for data instead of actually working with it. Their legacy data is growing faster than the costs of technology are dropping, which is driving total costs up to the point where they can no longer afford to backup all data. Furthermore, they've developed their own tool (fsview) and have done analysis of current utilization of data storage, and found as many as 18 redundant copies of files.

The primary issue is that the simple tools included with filesystems provide very limited metadata for managing data (typically file owner, group, size, and creation/modification/access times). Information such as project, laboratory, security classification, availability requirements, and lifespan are not available.This information is critical for managing efficient and cost-effective storage of the data, as it needs to be identified long after it's created when the original creator may not be available or may not remember the details of the data.

He quoted investment guru Peter Lynch's adage, "Know what you own and why you own it" as the guiding principle of data management. As step towards tackling the problem, the management of the Broad directed that all files be associated with funded projects. Matthew noted that there is an established field of solutions specifically designed to address this challenge: digital asset management (DAM). They are working with the iRODS software that is derived from the Storage Resource Broker (SRB) from UCSD Supercomputer Center. SRB and variants have made fairly substantial penetration into large-scale data management (I've previously talked to the folks at General Atomics, who provide a commercially supported version of SRB called Nirvana SRB).

But he said the technology is not really the challenge, the biggest change is the cultural change required of the scientists, who will need to tag their data as they are created. Some of the tagging can be automated, but there will also need to be other metadata provided by people. He said his approach will be to provide the service, and data won't get the usual services (backup, security, etc) until they have been registered in the DAM.

I'm very interested in these efforts as it's a natural follow-on to the whitepaper we are working on focusing on Research IT Infrastructure, which clearly demonstrates the challenges we face in the next five years, and the need for better data management.

Chris Dag from BioTeam - Trends from the Trenches

2010-04-22T09:10:00.002-04:00

Chris Dagdigian from BioTeam chaired the Track 1 Infrastructure - Hardware talks, and got some additional time due to the unfortunate loss of Phil Butcher from Sanger due to the volcano. Chris ran through the latest Trends From the Trenches presentation, and had some interesting updates.

He had expected blades to win the HPC hardware battle, but has not seen that come to pass, it's still a split field
Intel is currently the chip of choice, but AMD might be back in the game
BioTeam has done more Sun Grid Engine consulting in the first quarter of 2010 than all of 2009; he's not concerned about SGE's future following the Oracle acquisition of Sun
He got a laugh from the crown with "private clouds - still stupid in 2010". He notes that this is just marketing speak and doesn't really mean anything.
Public clouds, on the other hand, are very real, and close to being mainstream... he's a strong supporter of their use in the right situations.
DIY cluster/parallel filesystems have a higher risk of implementation failure rate due to lack of pre-sales planning and design, especially in smaller shops. He also recommended commercial solutions with formal support programs.
Clusters are increasingly utilizing fat nodes (32 core, 128 GB+ memory)
Petascale storage is no longer risky, and single namespace solutions are recommended
He expressed concern about the downstream analysis of data (such as sequencing) eating up storage capacity - while the HTPS pipeline is relatively easy to model, secondary analysis is much more difficult.

He had an interesting observation regarding communication between IT and scientists. He gave the example that scientists will often ask for 100% uptime and full data protection, but don't realize that the difference between five 9s and four 9s of uptime is several million dollars. He emphasized the need for bettter communication between IT and research, and that IT needs accurate accounting of IT costs so that it can explain the costs of services and facility

He argues that the DNA data deluge will get better, mostly because the sequencing vendors are becoming more efficient in delivering data from the instruments. I would agree that the per run sizes will stabilize, but as the costs continue to plummet for sequencing, it will drive much greater demand, thus continuing the pressure on storage and compute infrastructures.

He also talked about an issue that Jackson has had recent experience with, and that is the challenge of high-speed networking. He noted that moving large data around requires more than just big pipes and bandwidth. His experience is the number of hops between locations can have a huge impact on performance, as well as the tools and protocols utilized.

John Halamka on EHR

2010-04-22T08:22:00.002-04:00

"From the doctor's brain to the patient's vein." - John Halamka, CIO of Harvard Medical School, on the impacts of EHR.

Wednesday at Bio-IT World started out with a keynote by John Halamka, M.D., M.S., CIO of Harvard Medical School, and fourth person to have his genome publicly sequenced. John walked the group through the implications of hundred of pages of $30B Healthcare IT legislation. Regarding privacy concerns he said, "there will not be a massive database in the basement of the White House run by Sarah Palin." He said the goal is to go from 20% to 100% use of EHR in five years, and characterized fully implemented Electronic Health Records as improving the accuracy and efficiency of medical records - "from the doctor's brain to the patient's vein."

John also related an interesting story about their one and only data breach. It started with an employee looking at a particular clinical trial involving 4000+ subjects. They found the data very compelling, and made a copy on their laptop (encrypted), which was then forgotten. A year later the employee left Beth Israel Deaconess and went to UCSF, and in the process copied the contents of their laptop to a new unencrypted laptop (CA has less stringent encryption requirements than MA). The laptop was stolen by someone, pawned, when the pawnshop owner couldn't get the system to boot, he called Dell Tech Support. Dell, upon discovering the contents of the laptop, contacted Beth Israel, and the laptop was returned in 24 hours. He said that he spends $1M annually on information security for BID, and that they are attacked every seven seconds over the Internet, half of which come from eastern Europe and other half of which come from eastern Cambridge.

Some other points of interest:

Lab tests will start using controlled vocabulary to ensure consistency across providers.
Patients will be able to get a full copy of their EHR.
The Social Security Administration spends $500M annually managing paper records, which are subsequently digitized.

He also commented on the growing collection of wifi-enabled devices capable of measuring and reporting body telemetry. He is using a home scale which automatically transmits his weight, body mass, and other data to Google Health and Microsoft Health Vault.

Bio-IT World Keynote: How to Start a Drug Company

2010-04-21T07:01:00.001-04:00

"I will be shocked if there aren't drugs in the market in the next 10-15 years that target aging genes [and pathways]." - Christoph Westphal, CEO of Sitris Pharmaceuticals, responds to a question from Kevin Davies, Editor-in-Chief of Bio-IT World.

The kick-off keynote at Bio-IT World 2010 was given by Christoph Westphal, a doctor and scientist who has started a number of small drug companies. While most of them lost (or are losing) money, one was a widely-acclaimed success, at least for a time.

The conference was opened by Cindy Crowninshield, the conference director. One major challenge the conference has faced has been the need to find 20 replacement speakers due to travel disruptions caused by the Icelandic volcano.

The keynote was introduced by Ronald Ranauro, CEO of GenomeQuest, a company trying to carve out a niche in the next-gen sequencing data market with a SaaS offering they describe as "SDM" (sequence data management). It's not clear to me yet how they differ/integrate with LIMS solutions, but we'll find out more on Thursday, as I'll be meeting with them and another colleague from Jackson. Ron pointed to the exponential growth in genome data has a tremendous opportunity.

GenomeQuest is looking to aggregate 1 million public genomes.

Back to Christoph, who told the story of Sitris, which was eventually acquired by Glaxo-Smith Kline for $720M. They are working with Resveratrol, the anti-aging compound found in red wine. The talk focused on the process and components of a drug start that has a chance of making it.

This wasn't a topic of particular interest to me, but there were some interesting thoughts. By coincidence I had just had a long conversation with bandmate Jim Coffman, who is researching aging with sea urchin larvae at the MDI Biological Lab, on a ride back from band practice. It was great exercise for what I've learned in Genetics I and II over the last year. Jim's work focuses more on the TOR pathway (which is linked to rapamyacin, something being studied by Dave Harrison's lab at Jackson), but it seems similar to the SIRT1 pathway, which is regulated by resveratrol. The big picture here is that caloric intake affects these pathways, in that a calorie-restricted diet has been repeatedly show to extend lifespan in multiple organisms.

But that wasn't the interesting part of the talk, really. More interesting was the insights to the incredible pace of progress in this field of research. Fifteen years ago, Christoph noted, it was considered crazy that there were genes involved in aging; now it's a major area of research.

Some other conclusions he's reached that apply fairly broadly:

it's more about the people than the technology
good teams overcome failures
a powerful vision/idea will attract supporters

He also noted that there is debate about whether to share data and information, or withhold it for competitive advantage. He is very strongly of the opinion that it is more important to share data and show you're a thought leader than worry about proprietary issues.

Prepping for Bio-IT World 2010

2010-04-20T15:58:00.010-04:00

It's spring and I'm at the World Trade Center in Boston, which means it's time for Bio-IT World. Workshops started today and the main conference is kicked off with a keynote and reception later this afternoon.

I'm really looking forward to a number of talks, and am struggling with the usual conflicts. The conference has seven different focus areas or tracks and I'm interested in the first four - IT Infrastructure Hardware, IT Infrastructure Software, Bioinformatics & Next Gen Data, and Systems and Predictive Biology.

Track 1 (Hardware) will spend all day Wednesday on Scaling up for the Data Deluge, and then on Thursday look at Sequencing, Genetics Data Management & Grid Computing in the morning and Data Storage & Usage for Computational Tasks in the afternoon. Particular talks I'm interested in in this track are:

Wed, 11:00 - Sanger Centre's Perspective on Data Storage Challenges, Phil Butcher, Head of Systems at Sanger
Wed, 11:30 - Adjusting to the New Scale of Research Data Management, Matthew Trunnell, Acting Director, Advanced IT, Broad Institute
Wed, 2:15 - Improving Storage Efficiency for Unstructured Research Data, Richard Shaginaw, Project Manager, Scientific Computing Services, Bristol-Meyers Squibb
Wed, 3:45 - ResearchStation: A Bioinformatics Platform for Research Collaboration in Translational Medicine, Lynn H. Vogel, Ph.D., VP and CIO, Associate Professor, Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center
Thurs 11:00 - Pallas, a Computational Analysis Network, Charles Hurmiz, Director, Research Informatics, Information Sciences, St. Jude Children's Research Hospital
Thurs, 11:30 Making Systems and Services Easy: Secure File Sharing and Computational Portals, Shawn Houston, Technical Lead, Life Sciences Informatics, University of Alaska Fairbanks
Plus I'm presenting on IT Infrastructure Strategy in Support of Next-Gen Biological Research at 1:45 on Wed.

Track 2 (Software) spends Tuesday on Collaboration & Open Source Tools, Genomics Data & Wikis, and Semantic Web & Linked Data Technologies. Wednesday is focused on Information Exchange, Integration & Security. Items that catch my eye include:

Wed, 11:00 - Test to Best - Evidence for Collaboration and Science Driven IT as Criteria for Personalized Medicine, Michael Berens, Ph.D., Director of the Cancer and Cell Biology Division, Brain Tumor Research Lab, Translational Genomics Research Institute (ack! already a conflict with Track 1!)
Wed, 2:45 - Feature Presentation: The BIG Idea: Strategies to Achieve a Rapid-Learning Health System, Ken Buetow, Ph.D., Associate Director, Bioinformatics and Information Technology, National Cancer Institute (this talk spans Tracks 2, 3, 4, 6, and 7).
Thurs, 2:30 - Sharing Data While Keeping Control, Werner Ceusters, Professor, Director, Ontology Research Group, NYS Center of Excellence in Bioinformatics & Life Sciences

Track 3 (Bioinformatics and Next-Gen Data) focuses on Driving Biomarker Discovery and Translational Research on Wed morning, then Data Management & Integration Strategies on Wed afternoon, followed up with Application of Data on Thursday.

Wed, 11:00 - Leverage Emerging Technologies to Manage Genomic and Clinical Data, Stephen Friend, M.D., Ph.D., President, Sage Bionetworks. This first slot Wed is brutal. Sage is the non-profit off-shoot of Merck that looks very interesting.
Wed, 12:00 - Pipelining Your NGS Data, Nancy Miller Latimer, M.S. Senior Product Manager, Biological Sciences and Analytics, Accelrys.
Wed 1:45 - CASTOR QC - A Database Approach for Handling Large Genomic Data Sets, Marc Bouffard, M.Sc., Senior Bioninformatician, Montreal Heart Institute and Genome Quebec Pharmacogenomics Center
Thurs, 11:00 - Unbiased Prioritization of Mutations in Cancer Genomes, David Dooling, Ph.D., Director, Analysis Developers, Laboratory Information Management Systems (LIMS), and the Information Systems Groups, The Genome Center at Washington University in St. Louis School of Medicine
Thurs, 3:00 - Toward Meaningful Whole-Genome Interpretation with Open Access Tools from the Genome Commons, Reece Hart, Ph.D., Chief Scientist, Genome Commons, UC Berkeley QB3 and Center for Computational Biology

Track 4 covers Data Modeling: Enabling Systems Medicine, Data Generation: Good Models Start with Good Data, and Data Integration: Modeling Disparate "Omic" Sources on Wed. On Thursday the focus continues with Data Integration in the morning, followed by Data Validation: From Benchtop to Clinical Outcomes. There are only a handful of talks I'm interested in this track, and I've run out of time as the first keynote is about to start. And I haven't even covered the main morning keynotes. More later...

Jackson Lab Summer Student Wins Nobel Prize

2009-10-07T08:17:00.008-04:00

I realize this isn't really technology related, but we're pretty pysched here at work about one of our past summer students winning a Nobel Prize in Physiology or Medicine: "Jack W. Szostak, Ph.D., shares the 2009 Nobel Prize in Physiology or Medicine for his work in advancing understanding of telomeres, the protective “caps” at the ends of chromosomes that prevent damage to DNA. One of Dr. Szostak’s first experiences in conducting research was in 1970, when he participated in The Jackson Laboratory’s Summer Student Program." Many think of the Lab as the just the "mouse house", ie a supplier of mice, or a just a research lab, but our educational effort is just as important a part of our mission to improve human health.

Paper Mills to Green Data Centers

2009-06-05T09:57:00.013-04:00

Bruce Segee, Associate Professor of Electrical and Computer Engineering at the University of Maine in Orono, gave a presentation today at the Jackson Laboratory about a proposal to build an energy efficient regional data center in a former paper mill.

Bruce started his overview of the CIDER (Cyberinfrastructure Investment for Development, Economic Growth, and Research) submission to the Maine Technology Asset Fund (MTAF) as a proposal to "change the world" by rejuvenating former paper mill space as a green energy platform. It involves partnerships with just about every technology related organization in the state, and targets the facility near Old Town, Maine.

View Larger Map

The facility has 40 Mw of on-site green power in the form of 3 generators (hydro, biomass, and recovery boiler), 135,000 square feet of space, and tremendous cooling capacity from the river. The onsite natural gas turbine can take advantage of the nearby Juniper Ridge landfill, which is generating 5 Mw of natural gas. The cost to produce electricity at the facility is roughly $.06/KwH , and the retail cost of power on the grid is $.22/KwH, so there is clearly opportunity for this to be a sustainable business model.

One ironic issue is that Maine river water is generally too cold for efficient use in the paper industry, as it requires more energy to boil it for the paper making process. This liability becomes an asset for data center cooling.

The cluster they are targeting to build would have 1024 cores and would hopefully make the Top500 list. The computational capacities would be of interest to multiple industries in the state including aquaculture and marine, composite materials, precision manufacturing, and forestry and agriculture.

The location is desirable as Maine does not have a good dispersion of carrier-neutral data centers - most are concentrated in the Portland area. The feasibility analysis finds the idea of selling data center space consistently profitable, and does not propose to sell compute cycles.

Bruce notes the facility's connection with the University will help develop the state's IT staffing resources and expertise - this is critical to the state's technology industry which otherwise has to compete with Massachusetts and other New England states for talent.

Bruce reviewed progress on the proposal, as well as 8 other proposals that all leverage this facility. An announcement of the MTAF funding status of CIDER is scheduled for Monday.

Bruce then reviewed the regional network facilities and issues, and noted that there is great opportunity for Maine to be the crossroads between the U.S., Canada, Europe and the rest of the world. There are currently two pending proposals with the NSF and NIH, with a longer term goal of a "three-ring binder" built with stimulus funding. The network would consist of three network loops within the state running east, north, and west with the Orono facility at the center.

All in all, some very interesting ideas which can hopefully lead towards a vision of Maine becoming another technology hosting region for the country.

Clifford Reid on Personalized Genomics

2009-04-29T11:49:00.003-04:00

Clifford Reid, CEO of Complete Genomics

Kevin Davies opened up the second full day at Bio-IT World 2009 with thanks for the audience for solid participation in tough economic times - attendance at the conference is up compared to last year, which will help the group in their efforts to kick off Bio-IT World Europe in October.

Complete Genomics is "the Netflix of Next-Gen."
- Kevin Davies

Kevin then introduced Clifford Reid for the day's keynote, titled Personalized Genomics - The Impact of Large-Scale Human Sequencing Projects, who began his talk with a review of the costs of sequencing, which started out dropping by 2x per year until 2007, when it began dropping by 10x per year. This drop is the result of the confluence of three technologies:

Bio - Oligos (synthetic DNA), enzymes, flourescent molecules, DNA amplification
Nano - Photolithography, nano-robotics, CCD optical systems, ZMWs, nanopores
Info - Moore's Law (HPC), digital image processing, informatic insight: short paired ends (need to be able to make long reads)

Complete Genomics' approach includes manipulating the DNA to make it easily readable - they start with 500 bases, circularize it, then insert adaptors. These are combined into DNA nano-balls in a test tube, which are then dumped out onto a slide where they self-assemble into a square grid. The grid can be aligned with the imaging CCD pixels, so no pixels are wasted. The slide can hold an entire human genome, and will in the near future be read in a half day.

Sequencing a slide currently costs $5000, with the reagent costs at $1000. The chemical component of sequencing used to be the major cost; now that cost is down to hundreds of dollars per slide, and the costs of imaging and compute are the major factors. As this progresses, the data sets will get huge - 60 TB of images and 1 TB of processed data, requiring thousands of CPUs to process.

Complete Genomics is working in a new vendor model, as an information service provider, not an instrument vendor. They are focusing on scaling through continuous manufacturing technology, they are half a sequencing company and half a computing company, and they rely on two key distribution technologies: FedEx for atoms, and the Internet for bits. This is driving a new user model, the instrument-less genome research center, which are analogous to the fab-less semiconductor firms.

CG's five year mission is to build ~10 genome centers around the world and sequence 1 million human genomes.

The impact of this revolution will mean that academia can tackle large human populations and orphan diseases that aren't otherwise commercially interesting. BioPharma will see a reduction in costs and will attack cancer head-on. Agriculture and energy fields will see an explosion of new, economically viable genomic studies on plants and microbes. Personalized genomics, already in the early stages of use, will continue to grow rapidly.

The field of genetics research is moving from instrument-centric efforts, to a data-centric focus for the next five years, and eventually to a post-discovery action-centric world.

Cliff then noted that major leaps in science comes with advancement in measuring tools that allow new hypotheses to be tested. He took the room back some 400+ years to the invention of light microscopy, which overhauled our view of the world, but noted that it didn't do much for medical progress until the improvements in the 1870s that enabled a view into the cell. The cause of tuberculosis was subsequently identified, and there was more medical progress in 3 years than there had been in the previous 300 years. High-throughput, low cost sequencing will enable large-scale complete human genome studies - the next five years will see the investigation of the genome with a high-resolution gene microscope, and it will do for cancer what the light microscope did for tuberculosis.

Next Generation Sequencing Data Management & Analysis

2009-04-29T08:00:00.008-04:00

Melissa Kramer of CSHL and Matthew Trunnell of The Broad

The first full day of Bio-IT World Exp 2009 included an interesting panel discussion with mid-to-high end users of next generation sequencers. Moderated by Gerald Sample from BlueArc, it included Melissa Kramer from Cold Springs Harbor Laboratory, Matthew Trunnell from The Broad Institute, and Bruce Martin from Complete Genomics.

CSHL is the smallest operation of the three, with nine Illuminas. The staff of 11 running their sequencing process uses BlueArc systems for storage and a 2000 core cluster of IBM blades for compute.

The Broad is one of the largest sequencing operations in the world, with 47 Illuminas, 8 SOLiDs, 10 454s, and close to 4 PB of storage (mostly Isilon and Sun).

Complete Genomics is working on next next-gen sequencing, which requires very high throughput. Their sequencing technology is built in-house and is image-based, they are running Isilon storage to handle the active sequencing, plus a cheaper tier for parking before handing over to the customer. Thanks to the hand-off, they don't have the long-term storage concerns of most labs. They are however are continuing to be challenged by the storage I/O needs of the instruments - he characterized the problem as "severe", and said they are resorting to custom engineering and dark fiber to address it.

Matthew said that in designing storage for NGS, it's important to distinguish between working storage for the pipeline versus what is needed downstream for later analysis and retention.

The group discussed the changing nature of what is considered "raw" data, that increasingly the image or initial data is no longer kept, and the initial analysis of the sequencing process is now considered raw. Melissa noted that CSHL started out keeping the raw data, but have dropped that practice due to the storage constraints.

The Broad has been struggling with how to manage the huge amounts of data - they have 1000+ filesystems and billions of files. Migration policies for moving the data between different tiers of storage based on filesystem information is not straight-forward or sufficient; there is a critical need for better metadata describing the data. Bruce commented that they don't try to figure out what to archive, they figure out what to delete. Melissa noted that they are moving some of their data to tape for long term storage, Bruce cautioned that if you use tape, make sure to have multiple copies as "tape dies over time".

Matthew said that the compute and working storage will need to move closer to the instruments as they provide greater capacity. Matthew noted that moving data is a problem because the networks is not getting faster as quickly as the data is growing - sneakernet is still frequently in use.

Bruce agreed and said that it's much easier to build out compute than to build out storage. He agreed with Chris Dagdigian's keynote that analysis data will eventually go one-way into the cloud.

UPDATE (5/14/09): BioInform has a nice article up covering NGS data storage issues as discussed at Bio-IT World.

Eric Schadt on the Systems Biology Revolution

2009-04-28T08:21:00.012-04:00

"There are no such things as pathways, there are only networks."
- Eric Schadt

Tuesday morning started out with Eric Schadt, Ph.D., Executive Scientific Director, Genetics, Rosetta Inpharmatics/Merck Research Labs; Vice President and Chief Scientific Officer, Sage, with a talk titled Integrative Genomics.

Schadt founded and lead the genetics department in molecular profiling at Merck's Rosetta subsidiary, and is considered a pioneer in integrative genomics. While still at Merck, he is transitioning to Sage, "an open access, integrative bionetwork evolved by contributor scientists working to eliminate human disease." Sage will take the massive amounts of data Schadt has created at Merck and put it into the public domain. Schadt's vision is for Sage to the be the Google of biology.

Eric provided a brief review of sequencing research, and noted that the avalanche of genetic data doesn't really explain underlying mechanisms - the data alone is not delivering the breakthroughs some thought it would. We can see the patterns, but don't understand what is driving them. As an example of the how knowing the pattern is not enough, he put up a cartoon of a fat guy sitting in a lounger walking his fat dog on a treadmill, because studies show that there is a correlation between the weight of pets and their owners.

He then went through a relatively technical discussion of his research, noting how they discovered there was a huge network of gene interaction not only within a tissue but between tissues, and that these interactions had a demonstrable impact on health.

He had some nice visualizations of this activity, including an interesting diagram with various tissues and their associated genes arranged in a circle, and then lines representing interactions within tissues (on the outside of the circle) and those between tissues (inside the circle). It clearly shows equal if not greater interaction between tissues. These and related visualizations revealed that disease in one tissue may be driven by changes in another tissue. Later, when asked about the possible mechanisms for this communication, he said it's not understood, the endocrine system can't explain it. He has a hypothesis that new signaling mechanism are yet to be discovered, possibly cells that can communicate network state.

Gluster on commodity hardware

2009-04-27T16:15:00.003-04:00

I had a long, winding, and typically interesting conversation with Jacob Farmer from Cambridge Computer yesterday afternoon. One of the favorite topics for bio-IT infrastructure folks is how to make good use of Sun's Thumper (aka Thor) systems, which are extremely attractive storage systems from a capital cost perspective, but aren't a complete package. Many organizations have started with one or two and then grown out to many only to discover they are expensive to operate and maintain.

Jacob said he has been looking at using Gluster, a free, open source package which "is a cluster file-system capable of scaling to several peta-bytes. It aggregates various storage bricks over Infiniband RDMA or TCP/IP interconnect into one large parallel network file system. GlusterFS is based on a stackable user space design without compromising performance." It sounds like some organizations are having success pairing Gluster with Thumpers/Thors, though one person I spoke with said they had some issues with the administrative tools and interface.

It looks like an interesting platform that bears watching.

Research Computing and Infrastructure Technology

2009-04-27T15:58:00.010-04:00

The opening keynote at Bio-IT World Expo 2009 was given by Chris Dagdigian from BioTeam, titled Research Computing and Infrastructure Technology. Chris was introduced by Rudy Potenzone, Ph.D., WW Industry Technology Strategist for Pharmaceuticals, Microsoft Corporation, who noted in his remarks that "there will be more data generated in the next five years than in the history of mankind."

Chris is known for his 90-slides-in-30-minutes "Trends from the Trenches" presentations, however this was a somewhat less manic version of that talk. First topic was virtualization, which he says is the lowest hanging fruit in the infrastructure. He talked about a west-coast campus that ran out of power in the their data center, and in response built a "virtual colocation service" that recovered facilities, lowered costs, and provided more flexible services to users.

He had an interesting observation that the data deluge is not looking quite as scary as it was even last fall, not because the technology is coming to be rescue, but rather because people are realizing that there must be "data triage", or data management - we just can't keep it all. Furthermore, in the world of next-gen sequencing, he argues that infrastructure is not the gating element, it's the chemistry, reagent costs, and human factors that are the bottlenecks to the throughput.

In the last six months, BioTeam has put up their first 1 PB filesystem - he had a screen grab from a df command showing "1.1P". He really likes the "P". He noted more and more customers are not backing huge systems up - one customer has 50 TB of Isilon storage for research use, and they don't back it up.

He talked a bit about cloud computing and storage, and several times noted how much he likes James Hamilton's blog. James is with Amazon, which Chris says is the cloud - all the other providers are several years behind. Chris noted that James has said that the cloud storage providers can provide 4x geographically distributed storage for $0.80/GB/year, which he says is less than any organization can provide data in a single location, much less distributed. He said those kinds of economics are going to drive all data, even huge data, into the cloud. The problem that needs to be solved at the moment is that there is no good way to get large data (ie 1 TB/day) into the cloud, but he said Amazon is working on this and this will be overcome as well.

Looking out on the near horizon, Chris noted the recent release by Google of videos of their 2004 data center technology, and asked the question, if that's what they were doing five years ago, imagine what they and Amazon are doing now? The economics and competition related to these huge facilities is driving incredible, but secret innovation. Slowly these innovations are starting to leak out, which is a good thing for the rest of the field. One example are the rising operating temperatures of systems, and the huge energy savings associated with every extra degree hotter the facilities can run. Pushed by big customers, Dell is now offering systems warrantied for operation at 94F, and Rackable offers systems that are supported for 104F.

Lastly, he said he thinks federated storage is on the horizon, and referenced the recently formed partnership between BioTeam, Cambridge Computer, and General Atomics to deliver GA's Nirvana storage platform.

Headed for Bio-IT World '09

2009-04-23T08:07:00.008-04:00

I'm excited to find myself with a last-minute change of plans that has me headed to Bio-IT World Conference & Expo '09 next week. It's been a number of years since I've attended, and from the look of the agenda, they've made some major progress. I'm going to be focusing on Track 1 - IT Infrastructure & Operations, which has some great sessions lined up. I'm looking forward to talking to Matt Trunnel from the Broad Institute again, those folks are involved in supporting next-gen sequencing at a truly mind-boggling scale - they have something like 30 sequencers and just announced they were acquiring another 22! This should put them close to needing to deal with something like 10 TB/day of storage. It will also be interesting to hear from the BioTeam folks, who seem to have built a pretty good reputation in the Northeast for working in the life sciences space. Wednesday's keynote from Clifford Reid, CEO of Complete Genomics and the following panel session on personalized medicine should also be interesting, as the lab where I work has also been focusing on personalized medicine for some time. It will also give me a chance to catch up with Jacob Farmer from Cambridge Computer in person, one of our trusted storage advisors.

We Sleep to Prune the Brain

2009-04-02T16:41:00.002-04:00

In the process of caring for plants for many years (I collect orchids and bromeliads), I've found a number of parallels between their lives and mine. For example, their overall health can change rapidly for the worse, but only long-term, consistent, persistent attention and cultivation will result in an exemplary speciman. I've the same is true with my own health - it takes months of consistent attention to diet, exercise, sleep, and stress to feel truly excellent.

So it was with some interest that I ran across this research that suggests sleep is designed to prune the brain of unneeded synapses:

Sleep's core function, Cirelli and Tononi say, is to prune the strength or number of synapses formed during waking hours, keeping just the strongest neuronal connections intact. Synapse strength increases throughout the day, with stronger synapses creating better contact between neurons. Stronger synapses also take up more space and consume more energy, and if left unchecked, this process—which Cirelli and Tononi believe occurs in many brain regions—would become unsustainable.^2,3 Downscaling at night would reduce the energy and space requirement of the brain, eliminate the weakest synapses, and help keep the strongest neuronal connections intact. This assumption is based on the principle in neuroscience that if one neuron doesn't fire to another very often, the connection between the two neurons weakens. By eliminating some of the unimportant connections, the body, in theory, eliminates background connections and effectively sharpens the important connections.

Cool stuff!

IT Governance: Prioritizing Projects

2009-03-14T09:04:00.006-04:00

We've been working on building a consistent, simple process for evaluating and prioritizing requests for IT projects. Historically there seems like there has always been an order of magnitude more projects than there are funds or staffing to tackle. But how to sort through this onslaught of needs to sort out the real priorities?

We've used evaluation matrices for some time to facilitate structured conversations and make decisions about hiring staff and for selecting IT products. The matrices ensure that the information needed to make a decision is complete, and provides the opportunity to capture the relative values of criteria through weights. In poking around the web, I found several processes like this one that use a similar process for reviewing projects. Subsequently we've develop a relatively simple process that looks at both reward and risk associated with a request, and tries to make the scoring as quantitative as possible.

The fascinating part of this is that running a collection of requests through such a tool can be quite enlightening. For example, one of the first things you discover is that often requests are too vague to score accurately, and that they need to be broken down into smaller efforts that start with a feasibility/analysis stage. This helps to explain why prioritizing always seems so hard - it's because in many cases there just isn't good information to make a decision!

You may also discover that small projects with quick turnarounds, small resource needs, and limited risk score well. To a certain extent this makes sense, and lines up well with the principles of good project management.

The most important thing in my mind is that it provides a way to have a thoughtful discussion about priorities - it's critical not to let the tool take over, it needs to facilitate the real issue, which is clear communication.

My first iPhone Practice App

2009-03-14T08:23:00.005-04:00

I spent some time recently mucking with the iPhone SDK. I built this calculator from a tutorial I found after spending a fair amount of time wading through the materials on Apple's Developer site. First, I'm not a coder by any stretch, I have no experience with C, C++, objective C, what little I know is from Basic and Pascal from 20 years ago.

The iPhone is an amazing piece of hardware, and I have even more respect for some of the apps I have running on my phone now that I've been through this process. I typed the code in to get familiar with the editing interface, I managed to find and fix five bugs the compiler caught (mostly typos), however I almost got stumped by a seg fault once the app built and ran. After sleeping on it, I realized I had probably hooked up the code incorrectly in the Interface Builder (the instructions weren't very clear on that part). So I looked at another app that worked, and discovered my mistake.

At this point I can probably create a very simple, relatively static app that provides information (like the first aid apps, for example). But anything beyond that which involves more substantial logic and/or use of some of the cool hardware like accelerometer or GPS would require a lot of training in objective C. My understanding from my reading so far is that managing memory on the iPhone is much more manual than other environments, and can be a major issue if you're not careful about cleaning up. Probably explains why my phone runs better if I reboot it every once in a while.

Apple's desire to control the quality of apps in the Apps Store is understandable - one of the most attractive things about the iPhone is its immediate, consistent usability. Yet it's proving to be difficult to scale. There are something like 25,000 apps in the store now, and the process for getting them approved has slowed down dramatically. Plus there is talk of a Premium Store for apps costing $20 and up. How this will play out as the G1, with its open approach, or the RIM or Microsoft stores get going will be interesting. Support for Flash has long been a sore spot on the iPhone, as it would mean Apple losing control over apps. Yet it would open up the development environment to a much wider market. One thought I've had that might resolve this conflict for Apple is to provide something like HyperCard for the iPhone. I always thought HyperCard was an interesting, multipurpose tool, and it would be great to have that kind of flexible swiss army knife paired with the iPhone hardware.

MultiTouch Table Proof of Concept

2009-03-13T13:07:00.008-04:00

I got a basic proof of concept multi-touch table built this morning from stuff I scavenged at work (box from Shipping, tracing paper from Engineering, iSight from Desktop Support). It's pretty rough, but does work well enough to demo the principles.

I'm using NUI's tbeta software, they also have a video with the construction directions for the hardware, which took maybe 30 minutes to setup.

It's pretty twitchy, and is very much dependent on the lighting environment. Moderately bright diffuse light seems better than direct bright light.

The Grid is Dead: Follow-Up

2008-12-05T13:18:00.003-05:00

I posted earlier about Arnie Mile's presentation at the Sun HPC Consortium meeting in Austin before SC08, this is the promised follow-up now that I have a copy of the slides.

Arnie's main point is that while the grid is dead, the need and associated issues remain. There is a still a need to share resources across administrative domains, and that raises a host of challenges (registration, discovery, security, etc). The current effort to build a one-size-fits-all solution (ie Globus) has worked for a handful of large government sites, but otherwise has been largely a failure, thanks to "nearly insurmountable scalability and complexity issues."

Enter Thebes, a consortium lead by Arnie and Georgetown aimed at addressing this situation, and will initially focus on authentication, authorization, and accounting. So far, they've published a first draft of a Resource Description Language (RDL), which is a single, harmonized language to describe jobs and resources. Slated for summer 2009 is a draft of a Resource Discovery Network (RDN), which is a robust, globally distributed peer to peer and hierarchical resource discovery network.

The consortium is actively seeking help, primarily in the form of developers, to continue their work.

20 Years of SC

2008-12-03T05:50:00.006-05:00

This being the twentieth anniversary of SC, they had a large exhibit in one corner of the convention center with some pretty interesting items. Each year of the conference had a display, including technology from the time as well as items from the conference.

A main attraction at the exhibit was a Cray-1 from the mid 70's, originally installed at Los Alamos. This system cost ~$8M and provided 80 MFLOPS of processing power. The MacBook Pro in my backpack delivers more than 200 times the processing power (16 GFLOPS), and that is only 1/100,000th the power of the current leading supercomputing cluster (RoadRunner).

There were also components from later Crays (the X1, from ~five years ago)

as well as a board from BlueGene-L from the San Diego Supercomputer Center.

They had some posters with stats on the conference, it's interesting to note that conference attendance was relatively flat during the ten years from 1991-2001, but that it's roughly doubled since then. Another chart documented an increase of five orders of magnitude in both processing power and number of CPUs over the twenty years.

My SC08 Gig

2008-12-03T05:33:00.008-05:00

I showed up a little early for my SC08 gig on Wed afternoon, as Woody Woodruff from IBM, who was playing before me, was listed as playing country music. And indeed he was - a selection of country and old bluegrass material. He kindly accepted my offer to sit in on a few when I knew the tune to help out with harmonies and some guitar solos, which was fun.

When my set rolled around, Woody hung on and played for a while with me, helping out with rhythm guitar and harmonies. I then finished up the set with some solo material. Glen was good enough to snap the picture at the top, thanks Glen!

I was followed up by a wonderful group playing classical. The music room made for a tremendously civil and relaxing addition to SC, and I went and talked to Vivian Benton,

the wonderful organizer of the room, about making it a permanent addition to SC. She said she was already there, and had requested that there be another music room at SC09, which will be in Portland.

Visualization Gets Touchy-Feely at SC08

2008-11-20T15:07:00.017-05:00

SC has always had some of the coolest visualization displays on the planet, and this year continues that trend. This year saw a big jump in interactive multi-touch systems.

This is the Lambda Table from the Electronic Visualization Laboratory (evl), "an interdisciplinary graduate research laboratory that combines art and computer science, specializing in advanced visualization and networking technologies."
One of the applications was created for the Minnesota Museum of Science to teach students how rain and water flows over terrain (apparently there is a wide-spread misconception that water flows south, instead of down). In this case, when you touch the screen, it rained on that portion of the landscape, and the water then flowed down the terrain. Another application on the device was a view of the rat brain cortex, which could then be zoomed in and out to a fairly high level of magnification.

There was also some of the more traditional techniques, where you manipulate the visualization with a handheld controller and glasses; in this case it is wireless...

and in this case it is a 3D joystick with feedback. The setup was built by the High-Performance Molecular Simulation Team with the Computational Systems Biology Research Group from RIKEN in Japan, and is a looking at protein folding. It includes a display in the back showing a protein and a target drug molecule in 3D, and allows the user (wearing special 3D glasses) to move the drug molecule around and in and out of the larger protein. All the while the joystick is providing feedback on the interactions between the drug and the protein, giving resistance and bumps as the molecules collide.

Cyviz was showing a gorgeous large display with 3650 by 1050 resolution generated by DLP projectors and their special blending technologies to provide a seamless image.
Next is a beautiful 64" prototype LCD monitor from Sharp in the San Diego Supercomputer booth, with 4096 x 2160 resolution.

There were a couple of other multitouch tables, one from the University of Amsterdam

and another from RENCI. The RENCI folks said it took them about six months to put their hardware and software together.

The SC08 Green500 BoF

2008-11-19T18:32:00.007-05:00

The SC08 Green500 BoF was led by Wu Feng from Virginia Tech. He started with a brief history for perspective. He then launched into the issues surrounding the creation of the list, a discussion of which is the purpose of the BoF. There were brief presentations from several vendors, folks from analyst IDC and journal HPCWire, and a couple of users.

I hadn't really intended to go to this session but tagged along with Glen (ironically because I needed to find power for my laptop). I tried to listen to the conversation, which got pretty energetic at times, from the perspective of a CIO/decision maker, and what they would want from the Green500. Here are my thoughts:

A single, simple number will be hard to deliver. There is simply too great a range of uses for HPC, both in terms of size and computational problem, to have a single number mean much of anything. CIOs want a single number, but will also understand the complexity of the situation, and might even be skeptical of a single number as overly simplified. Several in the audience suggested creating segments or classes - I think this is appropriate, probably based on the size of the system in Tflops.
The number should not have anything to do with cost or "value". While the vendors may want that, the Green500 should not evalutate value - let IDC, HPCwire, and ultimately the buyers do that.
The major challenge is sorting out what is part of the data center facility and what is part of the system. I don't see an easy answer here. With the CIO hat on, I would say leave the facility out of it, as that's a separate issue with separate challenges and opportunities (ie tax incentives for green buildings, etc). Just tell me how much electricity the system takes, and how much heat it rejects. If you want to try to improve your score by taking on some of the facility issues, I'm guess I'm okay with that as I expect you will be able to improve your score, but at a greater cost (which again I will evaluate on my own).
No CIO will make the decision to spend 5-8 figures on a Green500 ranking alone. They will ask their people, what can the system do, and what will it cost to acquire and operate it? The main gold of the Green500 should be to help vendors and IT staff have a conversation about energy efficiency. It should also help provide credibility to the final purchasing recommendation that the CIO sees. The CIO should be ensuring that the system meets the compute needs of the organization in a cost-effective and environmentally responsible way.

It was a very interesting discussion to listen to, and I'll be interested to see where things stand a year from now.

SC08 Data Lifecycle Management BoF

2008-11-19T10:26:00.003-05:00

The Data Lifecycle Management: ILM in an HPC World BoF at SC08 Tuesday afternoon was an interesting discussion of the issues surrounding the storage, archival, and management of large data sets. Sponsored by Avetec's Data Intensive Computing Environment (DICE), it was led by Tracey Wilson, Computer Sciences Corporation and DICE and Ralph McEldowney, Air Force Research Laboratory Major Share Resource Center.

Many in the audience, including folks from NASA and other large sites, had years of experience with this - they were past the initial challenges of simply get the capacity in place, and were now struggling with trying to figure out what data needs to be kept for how long, who owns it, how to find it back, how to continue growing the service with something resembling an affordable cost. At the heart of the problem is the need for users to tag their stored data with metadata that describes such things as the owner, contents, projected size, expected lifespan, etc. Major HPC sites are finding that storage needs are eating into funding originally aimed at HPC capacity, thus potentially limiting the compute resources available for research.

They listed some of the more commonly used solutions today in this general space, although each has different levels of functionality when it comes to handling the metadata associated DLM.

The group seemed to agree that user training was a major goal - users need to understand the critical importance of associating metadata with their storage. Some expressed frustration in getting agreement on this, however - there was discussion of how to provide incentives to drive the right behavior, as well as the suggestion of deleting any data after a period of time that does not have associated metadata.

One site provides disincentives through increased fees for inefficient use of storage - space that is requested but not utilized is charged at a higher rate, as is data that is retained beyond a certain timeframe.

There was general consensus that establishing and enforcing policy around data management was a must - the example of eDiscovery was brought up as justification for properly classifying data so that it could be located easily during the discovery phase of a civil or criminal legal case. Failure to be prepared for eDiscovery can cost as much as $15M for a single case. One person noted that policy was relatively useless if developed by IT - it should be driven by the business needs of the organization, ie the records management and legal needs, working in partnership with IT. Another person commented that there is high likelihood of a failure of the commons in the effort to develop policy if this is not driven from the top down. Most researchers will be certain that there is no risk to themselves re: eDiscovery, so have no personal motivation to participate.

SC08 Music Room

2008-11-19T10:15:00.003-05:00

I swung by the SC08 Music Room yesterday, as I'm scheduled to play there today (Wed) from 4:00-4:45. I was fortunate to catch a pro, Darcie Deaville, who was there with sponsorship from enParallel. It's a great room, very nicely done, and Darcie sounded great playing a variety of tunes on guitar and fiddle. She had been planning to bring a hurdygurdy, but it didn't make it. She did however have two fiddles in tow, one of which she keeps tuned to an opening tuning (F?) that she plays with drone strings to give a similar feel to a hurdygurdy.

From the SC08 Showfloor

2008-11-19T08:00:00.010-05:00

I started my usual walk through the showfloor yesterday after the keynote to get the lay of the land and try to ID interesting talks at some of the lab booths. The FermiLab booth always has cool stuff, last it was a cloud chamber where you could see the trails of particles. This year they have an interesting sculpture modeled on a dark matter detector. The actual unit is under ground, however it is approximately the same size as this. So far they haven't detected much and are working to make the detection wafers larger.

Update 11/20/08 9:05: I should have noted they are looking for weakly-interacting massive particles (WIMPs), and there is an interesting story over at Wired from yesterday reporting another group of researchers on the same hunt seem to have found something interesting.

nVidia is getting a lot of attention for their "personal" supercomputer. The numbers look great, but one has to keep in mind that, as Glen points out, these are not general purpose HPC systems.

Rich Brueckner over at Sun (which seemed to be one of the busier booths) was in chaps and ready to ride, but with good reason - he had brought the Java Chopper to the show:

It's interesting to note in Rich's blog that he is looking to add a SunSpot to the bike...

These are very interesting little devices coming out of Sun Labs, the research arm of Sun. They have a variety of sensors and I/O options (accelerometers, light detectors, temperature sensors, LEDs, push buttons and general I/O pins), they run Java, they automatically form wireless mesh networks to communicate, and they can run for months on a single battery charge. A Java chopper with a Java-embedded SunSpot cranks the geek meter up pretty high...

which then quickly thwacks back to the zero pin across the aisle at the Microsoft booth. They were working a golf theme, obviously, and had a video golf course setup:

My guess is that this attracted mostly sales people from other vendors, as opposed to HPC customers, who don't as a group strike me as major golfers. I don't think Microsoft marketing has quite the right line on the SC crowd... my condolences to the MS booth staffers who have to toe the line, to their credit they were doing the best they could with what they had to work with.

Live Blog of the SC08 Keynote - Michael Dell

2008-11-18T09:37:00.021-05:00

Here we go with the Welcome and Keynote for SC08. Michael Dell is the keynote speaker this year.

Patricia Teller from UTexas is the General Chair of the conference, and she welcomed the audience with the news that the conference is setting a number of records this year, including the number of exhibits, education attendees, and a total of more than 10,000 attendees this year.

This is the 20th anniversay of SC, and a video retrospective included a clip of the Seymour Cray keynote, where he joked that his 10" slide rule was the leading edge of computing power.

9:07 - There have been nine companies who have been involved in sponsoring all 21 SC conferences: Cray, HPCWire, IBM, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, NASA, NEC, Numerical Algorithms Group, and Sun Microsystems.

9:10 - Michael Dell is introduced.

Michael says it takes 20 Pflops to model human brain, which runs on 20 watts(!). Japanese are spending $1.8B on a 10 Pflop system.

9:18 - Dell is announcing today they are extending their partnership with nVidia to add Tesla cards to their precision workstations, which will deliver one Tflop to the desktop.

9:19 - 489 of the Top500 supercomputers are based on the x86 architecture.

9:21 - Video of the vis wall at TACC, which is powered by Dell gaming systems. They are using it to support a cancer researcher who noted that we have reached a point where we can generate 250 TB of data for a single cell. The picture is part of a rotating 3D model from the cancer research.

9:26 - Technology advancements 0ver the last five years - you get more Tflops with 90% fewer systems. We need to build petascale software to take advantage of petascale hardware.

9:30 - 70% of HPC budgets go to staffing and facilities.

9:31 - Facebook utilizes 10,000 Dell servers.

9:36 - Brief video - review of the various generations, baby boomers, X, Y... the next generation is the regeneration.

9:37 - Q & A - Michael clarifies that his reference to the brain at the beginning was not to suggest that we need to recreate the brain, but simply to compare current HPC to the brain. "There are enormous opportunities to improve the man-machine interface."

9:43 - Question about his vision for education. He responds that public education needs to be delivering students familiar and at ease with 21st century technology - "it's as important as reading, writing, and arithmetic."

9;46: Question about alternative energy. Normal desktop uses $120 in energy a year, new Dell system uses $6 year. This isn't a source of new energy, but it does dramatically reduce the demand. Also, Dell is one of the first companies to become carbon neutral - you'll see companies begin to compete in this area.

9:50 - Another energy question - how to push component vendors to improve? Dell's suppliers report back on their carbon emissions, it's one of the things that Dell evaluates them on.

9:51 - Keynote is done.

Best Conference Gear Award

2008-11-17T16:23:00.004-05:00

My neighbor in the SAM-QFS BoF session gets the award for best conference gear. Finding power in these hotel conference rooms is a constant battle - this little unit has three plugs and two USB jacks. Outstanding!

Glen is Blogging!

2008-11-17T16:15:00.004-05:00

I guess Glen (that's his left hand) got sick of my nagging (or was it encouragement?) and is also blogging over at Exploding Frog. He has a slightly different perspective on events, as he actually knows how to use HPC instead of just spew off acronyms and jargon, so make sure you add him to your RSS feed as well.

SAM-QFS BoF Session: Great for Backup Too

2008-11-17T13:54:00.005-05:00

Harriet Coverston, Sun Distinguished Engineer and architect of Sun's distributed SAN file system, led a Birds of a Feather session with users, Sun staff, and third party vendors on Sun Storage Archive Manager and QFS. It was interesting to hear from current users at Clemson, the Arctic Region Supercomputer Center, Mississippi State, and TACC, who are all putting these solutions to substantial use.

Clemson is using SAM-QFS not only for home directories and moving large data to their cluster (which runs Lustre internally), but also as a substantial addition to their backup environment. The SAM-QFS approach to creating copies of file as they come into the system position it to be much more scalable for very large storage. It also makes for much faster recoveries - in one test they were able to restore 9 million files in nine hours, when a test restore with their traditional backup system was still running at 24 hours. This is reminiscent of conversations we've had with the Friedrich Miescher Institute for Biomedical Research, who are also using SAM-QFS as a add-on to traditional backup services.

The fact that numerous users we have talked to have come to utilize SAM-QFS to solve backup challenges in their environments speaks well to the software's data protection approach.

Jim Pepin: Arpanet < iPhone

2008-11-17T12:37:00.006-05:00

Jim Pepin, CTO at Clemson, had some thought-provoking points about the challenges facing research environments. Similar to some of Ray Kurzweil's analysis about the rates of change for technology, Jim compared technology today to his start in the field in the 1970s, and noted that there has been five to seven magnitudes of growth in storage, compute and networking capacities over that time. He noted that his iPhone has more compute and storage capacity than the entire Arpanet did in the 1970s.

He also got a round of unsolicited applause from the crowd this morning for pointing out the value of SAM-QFS and chiding Sun spending too much time talking about ZFS, and not giving more attention to the widely used software for large scale archival storage.

Jim said that storage is in many cases moving closer to the user, with GBs of storage in laptops or in pockets on phones and USB drives. That conflicts with organizational drives to do a better job of organizing and protecting data, and vendor pushes to move data and systems into the cloud. He noted that the speed of light is not a suggestion, it's a law - we can't change it to make clouds work better. He went on to suggest that campus IT has come to think of itself as plumbers and not innovators, and that trend needs to reverse if we are going to successfully address these challenges. He listed several efforts under way at Clemson, including the broadening of IT support beyond the traditional Helpdesk out to power users and user groups.

Now It's Official: The Grid RIP

2008-11-17T11:17:00.005-05:00

It's official now, Arnie put it on the big screen. I was too busy helping with his demo to take notes on the talk, but he's going to send me the slides, so I'll update this post with more later.

Where's "Head" Bubba?

2008-11-17T08:24:00.011-05:00

Glen and I have been wondering where "Head" Bubba is... he has been at recent Sun HPC Consortium meetings, and as much as we're struck by his presence, we're even more struck by his absence this year. Enough so that we felt compelled to learn more.

To give you some sense of why this is interesting, this gentleman is the VP of IT Research and Development at Credit Suisse First Boston, has more than a passing resemblance to one of the greatest singers of all time, and who's badge (and it turns out legal name) is "Head" Bubba.

Turns out the more you look, the more interesting it gets. I hope his absence from this year's conference isn't the result of the downturn in the economy, or worse the impact of seven barrels of Jack Daniels. As someone who has kept kegs in the basement for the last 20 years, I know first hand that surviving large quantities of good beverages in easy reach is all about pacing. Plus I'm a bourbon fan (Basil Hayden's), so I'll have to ask him more about his experiences with the great Tennessee whiskey next time I see him.

Update 11/20/08 16:44 - He's Here After All - I ran into HB this afternoon outside one of the conference sessions, introduced myself and had a brief conversation with and one of his colleagues. "Head" doesn't drink, but gives away the bottles of Jack to people with creative technology ideas - he mentioned a couple of recent ones (individuals at Mellanox and I think Stanford), which I think is really cool. He suggested that maybe I could come up with an idea and get a bottle, which I said I thought was unlikely. I mentioned that I am a homebrewer, and his colleague suggested that perhaps I could improve on the venerable VAXtap, and I said I thought that was more in my league. I'll have to keep my eyes peeled for an old half rack coming out of the data center.

Update 7/1/11 - HB and JD - I haven't been back to SC since 2008, however I got email from HB this morning, looks like I've qualified for a bottle from his latest barrel! I haven't made any progress on the VAXtap, inspiring as the recent New York Times article about the surge in popularity of home brewing might be.

Tour of Ranger - Loud and Windy

2008-11-16T17:10:00.014-05:00

The Ranger cluster at TACC, the largest public research cluster in the world at 579 Tflops, is not your typical data center tour. The system took $30M and two and a half years to implement, with total costs of $60M over four years. Two sides of the data center have glass walls, making for a nice showcase.

Before going in, Glen gives us a tour of one of the blades. The cluster has almost 4000 of these, for a total of 15,744 processors, 62,976 cores, and 123 TB of memory.

When you enter the room, the immediate sensation is of an intense environment. It's very loud, and in the rows, very windy. The APC chillers I'm in front of are on each side of the blade racks, returning cooled air from the enclosed hot aisle. Unfortunately I don't have enough hair to really give you a true sense of it.

Here we see six SunBlade 6000 chassis in two racks, each with twelve blades. Storage racks with 1.7 PB of capacity coming from Sun Thumpers run the Lustre filesystem are at the ends of each aisle. Data can only stay on the system for 30 days, as they are creating 5-20 TB/day.

These are power distribution units (PDUs) for the cluster, which draws 2.4 Mw at peak load, or enough power for 2400 typical residential homes. At $.06/KwH, the annual power bill is ~$1M/year. There are no UPSes or generators for the system, though they are planning to add UPSes for the storage and network fabric. Also, notice the floor vents - there is room-based HVAC in addition to the in-row systems to manage humidity and the larger environment.

The cluster itself takes 2000 sf, however there is another 1500 sf needed for PDUs and chillers. The room overall is 6000 sf.

The enclosed hot aisles allow for much greater efficiency in cooling the tremendous heat load. The fire suppression is water sprinklers (dry pipe pre-action), however they had to add more smoke sensors and alarms to deal with the enclosed aisles, as there was concern someone working inside the closed aisle wouldn't hear or see an alarm.

This is one of two massive Magnum Infiniband switches, the world's largest such device, with 3456 non-blocking ports. It is so dense that engineering the cabling was a major challenge.

Ranger supports over 1500 users and 400 research projects, and has handled more than 300,000 jobs for a total of some 220,000,000 CPU hours. There are larger clusters out there, but Ranger gets kudos for its density, and for putting together a very highly performing system with a considerably smaller budget than the DOE labs.

Clemson has Good Experience with Sun Cluster Install

2008-11-16T12:35:00.004-05:00

James Leylek, PhD, Exec Director of the Clemson Computer Center for Mobility Systems (CU-CCMS) spoke yesterday at the Sun HPC Consortium Conference about their experiences installing and testing a SunBlade 6000 cluster. The system has 3,440 processing cores: 31 SunBlade 6000 chassis, 10 blades/chassis, with two Intel quad core CPUs and 32 GBs of memory per blade. They wanted to do stringent acceptance testing on the cluster - install the system and then run it at full peak for 72 hours straight. They were told it couldn't be done. The installation included putting together the entire compute grid (19 miles of cabling) in three days. The testing began with individual blades, then chassis, then portions of the cluster, and finally the entire cluster. The tests ran successfully over 130 hours and the entire project was completed in 16 days.

Large Scale Visualization @ TACC

2008-11-16T12:07:00.004-05:00

Kelly Gaither, Associate Director of Data and Informational Analysis, UTexas Austin gave an interesting presentation yesterday on the visualization components of the TACC Ranger cluster, which we'll be touring later today. Known as Spur, it is comprised of eight Sun servers configured with high end graphics capabilities providing 128 cores, 1 Terabyte aggregate memory, and 32 GPUs. It is integrated into the fabric of the Ranger cluster. Since the system went into production in October, they have 38 users with over 120 hours/week of interactive usage, including one user that produced 43 TB of analysis output from a single run. Yeesh.

Interesting History for the Austin Airport Hilton

2008-11-16T11:37:00.007-05:00

Glen discovered some interesting info on the history of the Hilton Austin Aiport, where the Sun HPC Consortium Conference is being held in. The building was originally the headquarters for the Bergstrom airforce base, and served as a strategic air command center during the Vietnam War, the Persian Gulf War and Desert Storm. It was rescued from demolition and converted to a hotel and convention center about ten years ago. It's one of the better conference hotels I've been in. If you follow the link, you'll need to click on the correct link in the left nav bar to get to the page.

Update Sun 11/16 21:44: The bartender says there used to be seven floors beneath the current lowest floor, and it was indeed one of three places in the US the president would have been brought during a crisis. Three or four of the floors have been filled in, however the remaining had to be left because of piping/ductwork/infrastructure. The area is currently closed and not in use by the hotel. She had a handout of the old building, which had an open courtyard in the center. The current atrium was created during the renovation.

Update2 Monday 11/17 9:33: I thought I'd see if there was any chance of getting a tour of the lower floors. I talked to a supervisor who was in the military and familiar with the building when in use by the military. The front door was originally on the second floor and there was a ramp that went up to that level. Also, despite his military clearances he hasn't been able to see the lower floors. Two of the floors were used by the hotel for awhile, however the City of Austin, which owns the building, had them move out of one of them. Oh well.

Andy Bechtolsheim: Flash Is Here, But Tape's Not Dead

2008-11-16T10:35:00.004-05:00

Andy Bechtolsheim, cofounder and Chief Geek at Sun, spoke about Sun's HPC Storage Roadmap this morning. Andy's presentations go at about one slide every ten seconds, so there was a lot of info, most of which I can't talk publicly about in detail. Generally speaking, he argues that compute is becoming I/O bound - CPU clock speed increases are gaining less and less because it's getting harder and harder to get data to the processors. Disk capacity has grown rapidly, but I/O has remained relatively flat. The answer to this problem is flash memory - performance is not as good as traditional memory, but still substantially faster than disk. The cost is coming down at ~50% a year, and now is at a point where storage systems can be built on this technology. For example, and SSD has 8000 IOPs compared to 180 IOPS in a 2.5" HDD.

Andy went on to note that Sun is building a line of storage based on three different approaches (SSD, PCIe, and DIMMs) that will provide very interesting options for very high performance storage. An early version of a storage system based on flash DIMMs will be coming out in a couple of days at SC08. The system is 1U with roughly half the density and 840X performance over traditional disk. It also caught my eye that the recently announced 7000 system gets 192 3.5" disks into a 42U rack with only 7 Kw power.

This gets more interesting in light of Sun's recent open storage announcement called Amber Road, which is aimed at taking advantage of ZFS to pool this flash based storage with lower cost and lower performance traditional disk into a hybrid system to provide better read performance and lower power utilization for the same cost.

Andy was asked by Jim Pepin from Clemson what the implications are for tape. Andy noted that while flash and disk is getting cheaper, so is tape. Tape also has other advantages, like very low power consumption, and "won't go away for the next ten years at least." When asked about MAID, he noted that ZFS will include features to improve the power consumption of traditional disks, but that generally MAID has issues are slow spin up and read times, as well as the wear and tear of shutting down and starting up drives.

The Grid is Dead

2008-11-16T09:43:00.003-05:00

Glen and I had dinner with Arnie Miles, Senior Systems Architect, Advanced Research Computing Adjunct, Assistant Professor of Computer Science at Georgetown. Arnie is working on next-generation middleware called Thebes, a collaborative effort supported by Sun to create a secure attribute-based infrastructure for distributed computational environments. Arnie is looking for development assistance on the project, and was interested to find that Glen is a Torque developer, and could potentially help with APIs to that scheduler. Glen noted that it might be a good opportunity for a collaboration with the Computer Science department at UMaine. Arnie was pretty emphatic that the term "grid" is dead, and is looking for a replacement - my suggestions were "condiment" or maybe "fascia". Arnie offered to come to JAX to present on this work, and talk about collaborating with us.

Hitting the Big Time in Austin

2008-11-16T08:15:00.006-05:00

We had a great Texas barbecue for dinner last night out at a ranch on the southwest side of town. Leeann Atherton and her band served up some great traditional country and western, and were good enough to let hacks from the crowd join in (Merle Haggard's Sing Me Back Home seemed like a good fit).

I had breakfast yesterday with Josh Simons, a Distinguished Engineer int the Sun Systems Group, and also an amateur photographer. He's posted more pics over at his Sun blog.

Sun HPC Consortium - Lustre doing well

2008-11-15T18:40:00.008-05:00

The upcoming release on Tuesday of the latest Top500 list, the Olympics of the HPC world, has good news for Lustre's market share, especially at the top of the list.

Keeping up with the RSS feeds

2008-11-15T15:09:00.012-05:00

I follow a couple of dozen RSS feeds with Google Reader, which has a great interface for the iPhone/iPod Touch as well as a full browser. Reader keeps stats on your reading, ie "From your 22 subscriptions, over the last 30 days you read 3,646 items, starred 8 items, shared 0 items, and emailed 2 items."

A couple of noteworthy news items:

Economic trouble comes home to Maine - Fairchild Semiconductor in South Portland is shutting down for Thanksgiving week due to economic slowdown.
EMC officially announces new "cloud" storage system, which may or may not be as revolutionary as EMC suggests.
Oak Ridge National Laboratory announces the first petascale cluster in support of research.
A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution. The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.
Sun announces layoffs of 5000-6000 (~18%) due to economic slowdown, CEO Jonathon Schwartz suggests their open source initiatives put the company in a good position to handle the downturn.
Electronic boarding passes on smart phones are being rolled out.
Verizon schedules Storm for November 21 release, $199.99 on contract
The coolest data center ever, complete with waterfalls and plants. Also, an older technology called heat wheels is finding use as a new, highly efficient way to cool data centers.
New "spatial operating environment" (SOE) ala Minority Report is announced - video is a must-see. See also a novel use of scratching a surface as a control method.
Speaking of spatial, you can now visit ancient Rome in 3D over at Google Earth.
In a shocking discovery, a new study by sociologists at the University of Maryland concludes that unhappy people watch more TV, while people who describe themselves as "very happy" spend more time reading and socializing. Looks like my friend Nestor from the plane flight is on the right track.

Okay so that was more than a couple.

Getting Started in Austin

2008-11-15T12:45:00.006-05:00

Travel yesterday was uneventful if a little long (11 hours) considering the distance. It's always interesting to look at technology in the hands of the public on these trips. The last couple of years Treos and Blackberries were the phones to have, it's amazing this time how many iPhones I saw, and not just with business travelers, but airport/restaurant/hotel staff as well.

I had an interesting conversation with my seat mate from Boston to Houston, a 19-year old Guatemalen who, less than an hour before the flight departed, decided to buy a ticket and go back home for his girlfriend's birthday. He was toting a first-gen iPhone and a MacBook, and used both heavily - he was calling, IM'ing and email friends and family, and working on homework. He's been using computers since he was 10, he and his roommates have a completely wired apartment, and they spend most of their time on the Net instead of on the tube. Interestingly, he is ditching the iPhone for a BlackBerry because a friend convinced him they are better for email and texting, which is what he uses it for most.

The Austin Airport Hilton (pictured above) is nice, network performance is decent. I just got signed in for the conference, and had to sign a non-disclosure agreement (NDA) for the entire event. I was talking with a Sun employee at breakfast this morning who is also blogging this, and we were talking about how the NDA makes it difficult to say much in a blog. I'll do my best to pass along info while honoring the NDA.

Don't Forget the Sun HPC Consortium

2008-11-13T08:11:00.005-05:00

This trip also includes the annual Sun HPC Consortium, which is traditionally the weekend before SuperComputing.

"The Sun High Performance Computing Consortium (SHPCC) is an independent, volunteer-organized, international group of member organizations that own or use Sun computer systems with emphasis on high-performance, technical computing, and visualization."

There is a pretty solid looking agenda this year, I'm particularly interested in Andy Bechtolsheim's Storage Roadmap presentation on Sunday, the tour of the TACC Ranger cluster (the largest non-government HPC system in the world, and the fourth largest overall), Clemson's Jim Pepin talk on large scale filesystems in academic environments, and the half-day session Monday afternoon with the architect of SAM-FS, Sun's large scale filesystem that we are evaluating for our large research storage needs.

Getting ready for SC08

2008-11-13T07:42:00.012-05:00

"The SC Conference is the premier international conference for high performance computing (HPC), networking, storage and analysis. SC08 marks the 20th anniversary of the first SC Conference, then called Supercomputing, held in Orlando, Florida in 1988."

The keynote this year will be Michael Dell, which hopefully will be interesting. The first year I saw Bill Gates, who was pretty good, but I think Ray Kurzweil has been the most interesting keynote so far.

There are two "technology thrusts" or themes this year:

"The Energy Thrust will focus both on the use of high performance computing in renewable energy and energy efficiency research as well as the challenge of best practices and technology trends aimed at energy efficient data centers. The Biomedical Informatics Thrust will focus on the use of grid and high performance computing technologies to support translational biomedical research, computational biology, large-scale image analysis, personalized medicine and systems biology."

There is also a Music Initiative, which I'm scheduled to be a part of. There is a music room where you can sign up for 45 minute slots, my gig is late Wed afternoon.

A Disruptive Technologies Exhibit will focus on "quantum computing, flash storage, cheap optical communications, and 3D chip stacking for 2015-2020." Could be interesting.

Lastly there are three Masterworks sessions focusing on real-world applications of HPC:

Goodyear's Loren Miller will speak on application of teraflop computing to tire design
Boeing's Doug Ball will discuss the use of CFD to the fuel-efficiency of the 787
Morgan Stanley’s John Storm and Prashant Reddy will discuss HPC on Wall Street

About 10,000 attendees are expected, and currently there are 338 vendors and research organizations registered to exhibit on the main floor. It's huge.