Posts Tagged systems biology
The Semantic Web of Life Science
Posted by peanutbutter in bioinformatics, life-science, semantic web on April 25, 2009
This summary was born out of a question on Twitter and percolated to FriendFeed, which was “Who is using RDF and integrating other resources at the minute and what are those resources? From this question, several resources were highlighted.
UniProt. The comprehensive resource of protein information is available as an RDF distribution and each Protein record has a corresponding RDF download option.
Phil pointed out Semantic Systems Biology, As systems biology is largely concerned with representing networks and interactions at a systems level, a language like RDF would seem an obvious choice to represent this type of knowledge, to aid semantic description and data integration.
Melanie pointed out the following resources such as Bio2RDF. This project aims to RDF-ize numerous public life-science resources using what they call a three step approach which they have developed. The following image illustrates some of the resources that are included in Bio2RDF.
The NeuroCommons project seeks to make all scientific research materials – research articles, annotations, data, physical materials – as available and as usable as they can be. As a result they have an RDF triple store which they encourage you to either contribute to or download and use.
For a more general overview of resources that exist as an RDF implementation, the Linked Open Data cloud provides a graphical summary of the resources that exists and the relationships between them.
If you know of any more life-science resources or projects using RDF, then please do comment below. Egon has indicated he is working on RDF-ing the NMRShiftDB and ChEMBL’s Starlight, and Andrew Clegg is considering a project proposal involving RDF. As a result a very interesting discussion ensued on FF.
The BioSysBio conference 2009
Posted by peanutbutter in bioinformatics, conference report on March 26, 2009
The premise of the BioSysBio conference is to
bring together the best young researchers working in Synthetic Biology, Systems Biology and Bioinformatics, providing a platform to hear and discuss the most recent and scientific advances and applications in these fascinating fields.
This years BioSysBio 09 has just taken place in Cambridge, UK. The program was more slanted towards synthetic biology rather than more traditional systems biology, which I think reflects the growing momentum that synthetic biology has gained in the past year. I think this is a good progress and I was secretley glad as I did not want to spend 3 days looking at massive network diagrams squashed onto power point slides.
This was the first conference I had been to that the organisers actually requested that we use the BioSysBio FriendFeed room and Twitter to communicate, so I did. Half way through the first day the organisers demonstrated the FF room, which seemed to exist solely of Allyson’s posts, and questions were asked if she was a blogging bot. When we did confirm there was actually a female at an engineering conference, she was thereafter known as the BioSysBio poster girl.
As ever Ally was monumental in her blogging during the conference and all her posts can be found here. At one stage Simon did try to blog her talk to the same detail and speed, but he just kept coming up withe excuses about the wifi being slow – eventually he got there.
This was the first time I attended BioSysBio and I thoroughly enjoyed the experience. In general all of the talks were of a high standard most notable for me were Allyson Lister’s talk on Saint: a lightweight SBML annotation integration environment, Christina Smolke on Programming RNA Devices to Control Cellular Information Processing, Piers Millet on Why Secure Synthetic Biology? and Drew Endy on Building a new Biology. It was also good to hear about improvements for the Registry of standard biological parts by Randy Rettberg and the wiki style community building of the product catalogue, or data sheet about each part.
There is no point in me re-posting coverage that has already been documented, so if you would like to follow what happened you can follow the #biosysbio twitter stream, the biosysbio FreindFeed Room, or if you want a more comprehensive overview, Ally’s blog.
This was also the first time I had used twitter (via tweetdeck) instead of Friendfeed to microblog a conference. This approach certainly generated alot of noise and random soundbites, and was probably a fast way to make notes. However, although everything is grouped under the #biosysbio tag, they are not grouped around a particular talk or discussion thread. I can’t help thinking that microblogging via FriendFeed would be more focused around a specific talk and provide a more focused discussion, as opposed to just covering what was happening second by second.
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