For the agenda of the short course please see here.

For more information about Bio-IT World Asia please see here.

• A commercial support team for Taverna has now been established within Eagle Genomics, increasing company revenues through sales of its new services and contributing to the business’s development and growth
• The knowledge transfer has enabled Eagle Genomics to meet clients’ specific Taverna business needs, by making bespoke enhancements to the product
• The partnership between the University and Eagle Genomics has led to a joint Technology Strategy Board funding bid, attracting £500,000 for a ground-breaking life sciences project which will use Taverna to dramatically speed-up gene sequencing analysis
• The increased availability of both quality support and customisation services for Taverna will enable commercial organisations to carry out more and better quality research at a competitive cost, contributing significant economic value.

Importantly, with Eagle taking the support reins, the myGrid team can focus on developing innovative new features to enhance the Taverna product line. According to Professor Carole Goble of the University of Manchester, "This project will be instrumental in improving our productivity and the delivery of our consultancy services; as well as opening up an opportunity to develop a product-based strategy that should allow us to enter new markets, and support our growth in those we already operate in."

The full case study can be read here.

The author raises three key points regarding what needs to happen next:

• CIOs across government need to recognise what has changed and stop hiding behind the comfort blanket of what has always been done before. That blanket is on fire.
• Big suppliers should see the smoke from that comfort blanket and recognise that the world of government IT has changed. They can no longer rely on delivering poor service for big money and get away with it. The customer approach is changing and they will need to change too, or be consumed by the flames.
• SMEs should embrace the opportunity they now have and bring their capabilities – speed, flexibility and low prices – to the government market. For the first time, government is ready.

His comments apply to his own experience in working with the US government, but they apply equally to the UK and I'm sure to many other countries as well. Anecdotally I know of people working in Singapore research institutes who routinely use their own personal laptops and Google Mail accounts on a daily basis as their corporate IT infrastructure simply makes it too hard to get anything done.

As an employee of a small(ish) company, I cannot agree more. The big players move too slowly and are too well embedded to be able to rapidly take up and implement new technologies and ideas. The world has moved on, so why shouldn't government follow? The only thing that stands in its way are its own existing IT suppliers.

I'm not alone in believing cloud computing, amongst many other technologies, is really the way to the future. Wired reports that Amazon's cloud already contains 1 percent of the entire internet and is growing at quite a pace. Cycle Computing's recent 50,000 core supercomputer built around Amazon's technology is proof that pretty much everything that is possible in a traditional data center is also possible, with a bit of effort, in the cloud. There will always be some specialised tasks that cannot be migrated to the cloud but it won't be long before that 1% turns into 2%, then 5%, then 10%. The longer government and other state-funded bodies (e.g. the NHS, universities, etc.) take to join in, the harder it will be for them to catch up with the status quo and make the most of this technology.

Could these same comments apply to big corporations with similarly wide-ranging single-supplier IT contracts? I'd be interested to hear your thoughts.

The Best of Show competition recognizes new products available at the Bio-IT World Conference & Expo. Of the 34 new products, twelve finalists were named in four categories, and the judges viewed their products and demonstrations at the event.

Richard Holland from Eagle Genomics was one of the judges to vote for winners:

-IT Hardware & Infrastructure Category

• Opscode Chef – For an open-source systems integration framework built specifically for automating IT infrastructure in the era of the cloud.

-Informatics Tools & Data Category

• Anzo Competitive Intelligence Solution by Cambridge Semantics – For a system to target information to the right people at the right time from the right sources.

-Web-based Services & Software Category

• CERF 5 by Rescentris – For an award-winning electronic lab notebook (ELN) software for life sciences research organizations.
  

-Clinical Trials & Research Category

• ClearTrial 4.5 – For a Clinical Trial Operations (CTO) software, purpose-built for clinical planning, forecasting, outsourcing, and project tracking.

For more information about the winners and the finalists please visit Bio-IT world website.

The first reason is that although there was an overall winner, there was not an overall single best solution for the problem that Pistoia posed – the compression of FASTQ data. Rather James authored several entries, each of which performed well on distinct sets of criteria that may be important to different users. Some centres may value fast random-access to data later on, in which case fast decompression is important. Other centres value archiving data quickly as it is produced and do not necessarily need to retrieve much of it later, in which case fast compression is best. Yet others may simply need to minimise disk space, in which case the best compression ratio is most important. It is very hard to achieve best-of-class across all these factors and so the Alliance chose to recognise James' efforts in producing a series of specialised solutions rather than one catch-all approach. Had it not been for the crowdsourcing/open-innovation approach used in this contest then this may never have happened – and the concept that it would be a good idea to do this may never have occurred to Pistoia or its members.

The second reason is that this crowdsourcing approach does indeed produce genuinely innovative solutions, but the legal problems in doing so can be prohibitive. The Sequence Squeeze contest worked because it required all entries to be completely open-source (BSD licence) and free of all commercial code, and for the entrants to warrant that this was the case, but users of the code (all source code is linked to from the contest website) will still have to be careful that if they use it then they are confident that the licence is valid and appropriate and that it does not contain any third-party private property. John Overington blogs at Chembl on just this subject, but his words do not apply just to crowdsourcing but to all open-source projects. Submitting an entry to a crowdsourcing competition is in principal no different to submitting code to an open-source project on the web. The author still needs their employer's permission if done on company time and still needs to check their code does not include any illegal third-party inclusions. The users of solutions developed by crowdsourcing methods need to treat them in exactly the same way as any other open-source project – i.e. with care, attention to detail, and due diligence.

Another crowdsourcing approach to solving a genomics problem caught my eye this week as well, admittedly though because it featured an old colleague of mine who emailed the article to me. Guillaume Bourque's team at McGill university in Montreal developed a computer game to improve the quality of comparative genomics research. The game requires players to match up colour-coded blocks between species – blocks that in reality correspond to similar genetic regions that may have been transposed or relocated at the point that two species diverged in evolutionary history. This is computationally difficult but easy to do by eye given the right information – so by crowdsourcing the alignment process in the form of a game, the authors hope to get a much more accurate picture of the rearrangement of genetic data through evolution of distinct species than is currently possible using computational approaches alone.

BOSTON, MA., April 23, 2012 – The Pistoia Alliance, a precompetitive alliance of life science companies, technology vendors, publishers, and academic groups, today announced the winner of the Pistoia Alliance Sequence Squeeze Competition. James Bonfield, a member of the sequence informatics team at the Wellcome Trust Sanger Institute, has received the US$15,000 prize for developing the best new algorithm for compressing next-generation sequencing (NGS) data. Bonfield will receive his prize at the Pistoia Alliance Conference in Boston at the campus of Thomson Reuters on April 24, 2012, on behalf of a prestigious judging panel comprising representatives from the BGI, Broad Institute, Wellcome Trust Sanger Institute, and the Pistoia Alliance.

Labs rely on compression to enable them to store data from NGS runs, which includes sequencing reads and associated quality scores. Yet compression technologies are themselves faltering under the data volumes produced by NGS. The Pistoia Alliance Sequence Squeeze Competition encouraged anyone with expertise in data compression to tackle this problem. Ultimately more than 100 entries were received.

The judging panelists evaluated five key dimensions of the competitors’ entries:

• Compression ratio (a measure of how much the algorithm squeezes the data)
• Compress time
• Decompress time
• Compress memory
• Decompress memory

The judges weighed three of these elements higher because of their pivotal role in real-world usage. Compression ratio and compress time impact how quickly data can be packaged for analysis and how easily it can be stored long term. Decompress time also received more weight in the judging, as it affects how readily scientists can extract value from NGS data sets. In addition, compress and decompress time were deemed important because of the role they play in expediting data transfer between proprietary datacenters and cloud-based systems for genomics storage and analysis, which are becoming increasingly prevalent in the life science industry.

Bonfield submitted a cluster of algorithms that all delivered high performance in the top three judged criteria. His approach considered the importance of preserving alignment data in addition to raw FASTQ output and employed fqzcomp as a FASTQ compressor and sam_comp for SAM/BAM output.

“The competition exposed two important elements: First, that the gzip algorithm that served as the competition baseline is actually quite sufficient for run-of-the-mill compression, and second, that it’s extraordinarily difficult to make huge improvements in all three of the judged dimensions,” said Nick Lynch, external liaison of the Pistoia Alliance and chair of the judging panel. “Tradeoffs were made, which means that ultimately a compression toolkit might be the best approach to handle specific workflows.

Bonfield praised the structure of the competition, which included an open “leaderboard” for tracking submissions. “I can confidently say my entries benefited by the open nature of the contest. In a closed competition with a score table only visible after the submission deadline, I might have sat back and waited for the results. Instead, seeing an entry beaten spurred me to improve my submissions,” said Bonfield.

The judges also praised the quality of entries received and the conversation sparked by the competition. “During the competition itself, entrants discussed ideas openly on a variety of forums, and many entrants are already talking about merging the best parts of their algorithms together to address particular sequencing workflows,” said Lynch. “This is what’s so special about the open innovation the Pistoia Alliance promotes—the end results are significantly better than what could be achieved by individuals acting alone.”

Other members of the judging panel were Yingrui Li of the BGI, Tim Fennell of the Broad Institute, and Guy Coates of the Wellcome Trust Sanger Institute. The competition closed on 15 March 2012 and was administered on the Pistoia Alliance’s behalf by Eagle Genomics Ltd., a bioinformatics services and software company. Michael Braxenthaler, president of the Pistoia Alliance, will award the prize to Bonfield at the Pistoia Alliance Conference in Boston at the campus of Thomson Reuters on April 24, 2012. Bonfield plans to donate a portion of his prize to the Wellcome Trust Sanger Institute and the remainder to the British Heart Foundation.

The gathering of Pistoia Alliance members will be held on the first day of the BioITWorld Conference and Expo (it will end before the opening plenaries). The conference will feature the announcement of the winners of the Sequence Squeeze competition, demonstrations of the Sequence Services Phase 2 pilots for NGS data, and discussions about new Pistoia Alliance portfolio projects.

The agenda for the day can be viewed here. Will Spooner from Eagle Genomics will be presenting our solutions at 12:45 along with Cycle Computing, GeneStack, Constellation and Hewlett-Packard. After the presentations an open discussion will follow.

The table is now available online! Visit:

http://elements.eaglegenomics.com/

Please visit the table's website above to download the PDFs.

The current version of the table is distributed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Eagle Genomics are conducting a second survey of current issues in operational bioinformatics.

We build on the success of last year's survey which polled over 100 worldwide responses from both industry and academia. A report detailing the results of our first survey can be viewed here.  See also Genomeweb's coverage. One of the highlights was that data integration was one of the largest technology concerns for the community, and while both academic and commercial groups relied to a large extent on in-house data centers, they were considering shifting to the cloud in the future.

We are excited this year to see how the field has shifted over the past 12 months!

In appreciation of your support we will enter all participants in a draw for a $100 Amazon voucher.

This should take no longer than 5 minutes.

Survey deadline extended to 20th May.

After the survey closes on 28th March, answers will be summarized and represented as a report freely available from Eagle Genomics' website. This report will be of great relevance to both policy makers and software developers as they plan for the coming decade.

To all who came, thanks again for attending. We hope you found it interesting and also managed to grab a complimentary Eagle mug. All who weren't able to come, this is the blog you might want to read  to catch up with speakers presentations. The links bellow will lead to the slideshare website. If you wish to receive a copy of the delegate booklet email Ivan.

Some of the symposium highlights:

• Nine speakers, from key fields who looked into the future of bioinformatics and shared their strategies on dealing with the massive amount of genomic data coming from yeast, plants, animals, human genomes and diseases.
• Well timed breaks, which allowed plenty of networking opportunities.
• Three exhibitors DDN, LGC Genomics and S3, who showcased their services and generated interest from the delegates.
• For Twitter fans there was hashtag #egsym12, which is now summarized in Storify.
• The initial release of the periodic table of bioinformatics elements. A blog is available here. Comments about the table are welcome.

The day began with Eagle's CEO David Flanders opening notes where he said:

"Following on the success of Eagle's first symposium and impressive line-up of speakers, the 2012's panel is equally well suited to discuss the problems many organizations now face with the growing volumes of data from next generation sequencing and related technologies. I am sure that the day will be enjoyable and educational."

-The first two presentations were from-

1. Ian Roberts, Curator, National Collection of Yeast Cultures, Institute of Food Research -"Data delivery from yeast genomics to industrial biotechnology: problems and perspectives"

• Ian's abstract

2. Dan MacLean, Head of Bioinformatics, The Sainsbury Laboratory (TSL) – "Just enough developed infrastructure"

• Dan's abstract

–2nd morning session with Tim Hubbard as the keynote speaker–

3. Tim Hubbard, Wellcome Trust Sanger Institute – "From Genome Annotation to Genomic Medicine" 

• Tim's abstract

4. Miika Ahdesmaki, Senior Bioinformatics Scientist,  Almac –  "A toolbox for high throughput in-dept analysis of omics data"

• Miika's abstract
  

5. Mario Caccamo, Head of Bioinformatics, TGAC – "A data warehouse approach for large genotype-by-sequencing datasets"

• Mario's abstract

–Then an hour's hot lunch – enjoying the sun outside–

– The most fitting "after lunch talk" was about food security by Mick–

6. Mick Watson, ARK Genomics (Roslin Institute) – "Out of the shadows – the future of bioinformatics"

• Mick's abstract
  

7. Jonathan Green, Head of Bioinformatics, Health Protection Agency – "Exploiting whole genome sequencing for public health microbiology"

• Jonathan's abstract
  

–2nd afternoon session–

8. Dr Paul Denny-Gouldson, VP Translational Medicine, IDBS - "Science at the Bench and the Bedside: Less of a Tightrope, More of a Super Highway"

• Paul's abstract
  

9. Alex Gutteridge, Head of Bioinformatics, Pfizer Neusentis – "Omics for cell therapies"

• Alex's abstract
  

Once again thanks to all who came and made the day great. We had very good feedback comments by the delegates and we are looking forward to our 3rd symposium which will be Thursday 21st March 2013.