About two weeks ago, tipped off by Neil, I heard about Google App Engine. I managed to get a beta account, and I’ve finally had a chance to do something (hopefully) useful with it.
In the absence of any quickly achievable ideas for a bioinformatics app, I ported over the OpenRef application I wrote on top of TurboGears a few months back.
Just like the original, the new app, ResolveRef, is essentially a RESTful way of doing PubMed queries.
Continue reading ‘Announcing ResolveRef on Google App Engine’
I’ve always found it interesting how people describe their jobs, particularly scientists. Sometimes I find the “inevitable dinner party question” (”So, what do you do?”) difficult. The answer typically requires knowing the background of the inquirer … if your job description is too technical, it tends to freak people out, and can often cause the evenings conversation to disintegrate into too much science-talk (yes, sometimes it’s possible to have too much science-talk). The safer option, giving a simplified very high-level job description geared toward lay-people, is usually unsatisfying and can even sound a bit insulting if you are unknowingly speaking to someone with experience in your field.
Overall, I think it’s really good practice to be able to describe your job (or “role”, or “work”) as a scientist at many different levels. It certainly helps me understand “what I do”, and can really assist in having the right words on-hand when writing grants, fellowship applications, abstracts and maybe even (gasp) press-releases, each that could be aimed at widely differing audiences.
What got me thinking so philosophically this morning ? A tongue-in-cheek quote I noticed on a lab head’s page describing his role in the research group:
Gets the big pay check, sits around waiting for results, drinks coffee, helps write papers and tells people to work harder.
I’m sure he does a little more than that … but I suspect there’s also a bit of refreshing honesty in that description. Probably every part is true, except the “sits around waiting” part. I wouldn’t try using it to describe your role on a grant application though 
Blogger has served me well for the last two years or so. When I started with Blogger, I’d never really blogged before, and decided that it was a good way to get going quickly. I avoided the free blog hosting on Wordpress.com because it wouldn’t allow enough customization of the templates. Today I’ve completed migration of this blog from Blogger to the Wordpress software … read on for the “how” and “why”.
New URL is:
http://blog.pansapiens.com/
Feed url is via FeedBurner at:
http://feeds.feedburner.com/YourBonesGotALittleMachine
(Don’t read on if you don’t like meta-discussion about blogging software …. I personally have become pretty bored with this type of post, but it has to be done once after changing URLs etc. The blogger who “Blogs about blogging” is akin to those hip-hop artists who only ever sing about hip-hop … sort of like eating your own … yeck !).
Continue reading ‘Migration from Blogger to Wordpress’
The Google Summer of Code project participants have been selected for 2008. I scanned the list to see how projects specifically aimed at the biosciences and bioinformatics fared:
- GenMAPP (Gene Map Annotator and Pathway Profiler), a tool for visualizing gene expression data on top of graphical representations of biological pathways.
- The NESCent (National Evolutionary Synthesis Centre) Phyloinformatics project, has range of potential projects to do with phylogenetic analysis, covering things like phyloXML integration with BioPerl and BioRuby, phyloinformatics web services and tree analysis using the MapReduce algorithm (with Hadoop).
- OMII-UK, which covers a range of tools including the Taverna Workbench for workflow design and execution.
- Also participating is OpenMRS, a medical record system aimed at developing countries.
There are also at least two platforms for cluster, parallel or grid computing on the list; I spotted the Globus Toolkit and OAR, but there are probably a few more in that that broad category (eg, OMII-UK oversees a bunch of Grid related projects too).
It’s worth noting that I’ve ignored a bunch of really important pieces of software that are less field-specific, but are actually lower level components of the platforms critical for most large bioinformatics projects. Things like Python, Perl, R, various Open Source databases, and collaboration tools like wikis (MoinMoin) and CMSs (eg Drupal) are also participating.
I don’t think coding for bioinformatics applications is as attractive to students as working on some of the other “sexier” projects available (eg the SecondLife client, or the Apache Webserver), but kudos to Google for letting a few bioinformatics tools into the fray. Hopefully the students who hack on them learn something, and hone their coding skills (you never know, they may even help improve these tools too ).
I see Lars Juhl Jensen has come up with a fun tag cloud of recently popular buzzwords in the biosciences. He calls it a BuzzCloud. The buzzword from the cloud I’ve noticed most lately is “Quantative Proteomics” … quantitation is a good goal for the field of proteomics to aim for, since IMHO it doesn’t really deserve the -omics prefix. “Omics” tends to imply the possibility of global proteome coverage, which proteomic studies rarely, if ever, achieve. But enough of the side-rants.
The way Lars’ BuzzCloud is constructed by extracting phrases ending in -ics, -ology, -omy, -phy, -chemistry, -medicine, or -sciences etc reminded me of a stupid little CGI application I wrote a few years back … the Biotech company name generator. When you take common prefixes like “Gene-”, “Pept-” or “Chemi-” and suffixes like “-omics” or “-agen” etc, it’s amazing how often Googling the name turns up a real honest-to-goodness biotech company.
Feel free to comment on any “biotechie” suffixes and prefixes that I should add … the hardcoded list in the script isn’t that long.
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