Here are the links that appear on the last slide.

• The Genome Center
• PolITiGenomics (this) blog
• LIMS Paper
• YAPC UR presentation

The Odyssey

So you may be asking yourself, how did he generate a movie of his talk? Even if you are not asking yourself that, I am going to tell you so that if you need to do it (or if I need to do it again), you can avoid a lot of hassle. This was all done on a MacBook using a slide deck created in MS PowerPoint 2008. First I tested screen capture using VLC. It took a few tries with the video settings to make it not look terrible (use H.264 at 1024 kb/s bitrate, 25 or more fps, MPEG 4 encapsulation), but the audio capture did not work. To compensate for the lack of audio, I did audio capture using GarageBand (podcast project type) at the same time I did the video capture. I then loaded the audio and the video into iMovie HD, synchronized the audio to the video, clipped the beginning and the end, and exported. This resulted in a fair quality product. Being stupid, I thought I could do better. I next tested recording narration in MS PowerPoint, but there didn’t seem to be a good way to export both a video of the slides with the recorded timings and the audio into a single format (not to mention it stupidly saves the audio in seemingly uncompressed files without an extension, one file per slide). So I imported the slides into Keynote 08, cleaned up the messes created by the import, recorded the slide show, and exported to QuickTime at high quality. This looked and played great in QuickTime so I went to upload it to YouTube. Sorry, YouTube has a ridiculous and arbitrary limit of 10 minutes for a video. Moving on to blip.tv (which, nicely, also supports Creative Commons licensing), I uploaded the video. After waiting for it to convert, I played it and noticed that although the audio was fine, the slides did not advance. Thinking something was wrong with the blip.tv Flash converter, I moved on to Vimeo. Slides didn’t advance there either. So next I checked the video by watching it using VLC and mplayer. No slide advancement. Trying to fix it, I went into the custom video settings when exporting in KeyNote, trying all sorts of combinations to generate a video that played well in VLC. Using various settings, I was able to get the slides to advance for a while, but eventually they would stop. Audio was always fine. I tried upgrading to Mac OS X 10.5. Still no luck (although in 10.5, VLC can capture from the iSight camera, so maybe audio capture will work in VLC now). I then recalled that the MPEG-2 on Mac was a little quirky (QuickTime won’t played decoded Tivo Series 2 video without first converting them to MPEG-4 using ffmpeg). As a last ditch effort, I imported the KeyNote exported movie into iMovie HD as an MPEG-4 project. I check to make sure iMovie HD played it correctly, then exported at full quality as an MPEG-4. This ballooned the size of the video from around 20 MB to over 110 MB, lessened the quality, and introduced a strange pulsing phenomena in the slides (probably due to compression degradation being corrected by key frames every second or so), but it seemed to play correctly in VLC and was higher quality than the VLC capture video. This video, uploaded to blip.tv, is what you see above.

Update: Here is how Lawrence Lessig screencasts.

Massively parallel sequencing platforms are generating sequence data at a rate that is rapidly overwhelming the informatics community’s analysis throughput. From large projects like 1000 Genomes to individual investigator labs with a single next-generation sequencing instrument, bioinformaticians are being bombarded with unprecedented amounts of data. To begin to address this issue, much recent bioinformatics research has focused on developing faster algorithms for alignment, assembly, annotation, etc., resulting in a proliferation of analysis tools. However, faster algorithms for traditional analyses are only one aspect of the recent bioinformatics explosion. The richness of data now available to bioinformaticians allows investigators to ask new types of questions requiring new algorithms and new approaches, e.g., in the fields of medical and population genomics. The data and tools explosion has created a dichotomy for the bioinformatician: perform high-throughput analysis on large volumes of samples while evaluating many different tools and analysis workflows. High-throughput pipelines are linear and static and require detailed tracking. Evaluating tools and comparing results from different workflows are non-linear and ever-changing (especially in the current environment of rapidly evolving sequencing technologies and analysis tools) and typically involve many false starts that are not tracked. To reconcile these contrasting requirements, we have developed a software framework for genome analysis that combines ease-of-use, detailed tracking and reporting, flexible chaining of tools to define workflows, results comparison, and scalability. The design of this framework heavily leverages the lessons we have learned in developing a laboratory information management system for high-throughput genome sequencing in an environment implementing continual process improvements. The result is a next-generation informatics framework that will allow bioinformatics tools and workflows to be part of the experimental design of sequencing projects.

Sounds exciting, eh? Looking at the other talks in the session, it seems I should not delve too much into the coding details and focus more on the motivation and high-level concepts used in our system.

Several other people from The Genome Center will also be attending and presenting. Our Director, Rick Wilson, will be giving a keynote address on Saturday. Co-Director Elaine Mardis will chair the always interesting New Genomic Frontiers plenary session (don’t make the mistake of booking that early flight, you’ll miss the best stuff). Todd Wylie and Jon Armstrong from our Technology Development group will be giving talks on miRNA characterization and capture techniques, respectively. Also, be sure to check out Dan Koboldt’s blog post giving a sneak preview of the poster he will be presenting about the performance of various short-read aligners.

Another major change in the GA2 is the addition of the IPAR computer. This system allows the analysis of images to obtain intensities during the chemistry portion of the instrument cycle. This means that it is possible to no longer have to transfer the 1.8 TB of raw images that the instrument generates during a paired-end run. Unfortunately, the IPAR runs on Microsoft Windows, breaking with the run-anywhere philosophy of previous versions of Solexa’s image analysis pipeline.

Here are some raw specs for a paired-end run on a GA2.

• 4 gigabases (Gb) of sequence
• 5 days
• 1800 GB of images
• 300+ GB for image analysis (Firecrest)
• 60+ GB for base calling (Bustard)
• 10-30 GB for sequence analysis and alignment (GERALD)

As you can see, this system approaches nearly 1 Gb of sequence per day. Unfortunately, with the name changed to GA2, we will probably not receive a free guitar with each instrument purchase.

• ssaha_pileup – ssaha_pileup is part of the SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) package. It uses the SSAHA engine for alignments and then uses ssaha_pileup to call the consensus base at each position, thereby detecting SNP‘s. You can find the source code and documentation on their FTP site.
• WikiLIMS – WikiLIMS is a laboratory information management system based on the popular MediaWiki engine. Basically the folks at BioTeam have created a few templates for MediaWiki allowing people to enter standard information about each sequencing, e.g., sample(s) information, cycles, instrument, and technician. Once those fields are populated, the user can the use then resulting page as an electronic lab notebook for the experiment. Clearly, they are targeting small labs with a couple or fewer instruments. Dick McCombie at Cold Spring Harbor Laboratory mentioned in his talk that their sequencing group uses it.
• Anno-J – Anno-J is very cool, Web 2.0 based software for annotating genomes. The author says it is not quite ready for release, but he is planning on releasing it as free/open source software. He hopes that will encourage others to design their own tracks and plugins.
• Glimmer – Glimmer is a system for finding genes in microbial DNA. It is not new, but it was mentioned at the conference so I thought I would include it.
• GISTIC – Genomic Identification of Significant Targets in Cancer (GISTIC) is a program that takes as input a variety of whole genome array data from cancer samples and identifies regions which are statistically likely to play a role in cancer.
• VCAKE – VCAKE is a short-read de novo assembler. We have found that VCAKE performs quite well when you are able to provide it with a sequence to nucleate contigs around. The authors are working on a color-space version for AB SOLiD data.

The best session at AGBT was on Saturday afternoon, Future Horizons in Genome Exploration (chaired by my boss Elaine Mardis). It started with an entertaining talk by Stephan Schuster about the mammoth genome. Mammoths are about as close to modern-day elephants as humans are to chimps. John Leamon from RainDance Technologies gave a talk on their very cool microfluidics platform, complete with cool movies (yes, movies not animations). The session ended with a presentation by Pacific Biosciences Founder and CTO Stephen Turner about their single molecule, real time sequencing platform. Think about sequencing an entire human genome to tenfold redundancy in a matter of hours. That’s a lot of data to analyze and store.