Uninspired? Attend PSB 2009 (virtually)

Christmas break too short? More tired after the holiday than you were before? Perhaps you’d like to be on a Pacific atoll; Hawaii, for example.

Cheer up – attend the 2009 Pacific Symposium on Biocomputing via the magic of FriendFeed. They’ve already had an excellent session on open science (more details here) and the fun continues through to January 9.

Thanks to Shirley, Cameron et al. for the virtual proceedings. Oh, and a belated happy New Year.

What I learned from Clay Shirky about science online

The “science online” community has somehow compiled a required reading list (thanks John!), from which many ideas and quotes are mined. I recently finished reading an entry on the list: Here Comes Everybody, by Clay Shirky.

I enjoyed the book – much of it was familiar to me, but it makes good use of specific examples to convey general principles. Of more interest to me is the application of these ideas to science online. Here’s what I think we can extrapolate from the book – and this is purely my personal interpretation.
Read the rest…

Vindication for video

Announced first via FriendFeed (of course), Moshe from JoVE is circulating an email with exciting news. I can’t do better than to quote it here:

JoVE, the video-publication for biological research, was accepted for indexing in PubMed and MEDLINE.

JoVE is the first and only video-publication to be included in these databases maintained by the National Library of Medicine (NLM). The decision was made by the NLM advisory committee, Literature Selection Technical Review Committee, which is composed of the authorities in the field of biomedicine, such as researchers, physicians, editors, health science librarians and historians. This committee evaluates the scientific quality of publications and typically approves only 20-25% of the applications.

Inclusion in PubMed/MEDLINE is a big milestone for JoVE, and for the scientific publishing in general. It demonstrates the official acceptance of new approaches to science communication, such as video online, by the scientific community. Overall, it will increase the interest of the scientists to communicate their findings in video, making biological sciences more transparent and efficient.

Well done to the JoVE team.

BioBarCamp wrap-up

The latest “unconference”, BioBarCamp, wrapped up today. Once again a FriendFeed room was used to great effect in providing coverage. I think it’s worth stressing that in addition to the “as it happens” aspect, FriendFeed provides a permanent, searchable archive that you can revisit to revise your notes and refresh your memory.

Further information is at the BioBarCamp wiki and Deepak has a nice summary of the back-channels and other, similar events.

Congratulations to all involved – sounded like an excellent event.

FriendFeed “best of” the week

The new best of FriendFeed feature is proving to be a hit. It also provides material for people who are too busy to write real blog posts. Here’s my top 10, according to FriendFeed, from the past 7 days:

Proteomics discussion from the science streamosphere

friendfeed CAI discussWe find ourselves wondering why codon adaptation index (CAI) is used as a measure of protein expression level in this article.

One answer is that CAI does correlate well with protein expression in many proteomics studies; but surely these same studies contain raw data with protein expression level? On reflection, I bet the answer is that it’s too difficult and laborious to access this type of data. There are plenty of papers that describe large-scale analysis of protein expression using proteomics, but the data are locked up in the articles or as inappropriate supplementary files.

Note to self: look into open-source software and standard data formats for proteomic data.

Around the open science, social web

This blog seems to become more about social networks/open science and less about bioinformatics every week. Perhaps that’s no bad thing. Here’s a few highlights from the activity stream this week.