Yes! Why should the evolution people have all the fun with their blog carnival? (After all, it is only a theory.) It’s time for bioinformaticians to show what we are made of, and to have a carnival of our own. Bio::blogs had a good run some time ago. I decided to reconnect what is hopefully now a larger and more networked community under the title of Bioinformatics Blog Carnival.

Northampton: monument to Francis Crick, born in Northampton. Copyright Ian Rob, licensed for reuse.

Programming

For many new bioinformatic programmers, there is a question of which Bio* package to choose from. The Bio* packages (Biopython, BioPerl, BioJava and BioRuby) are open source licensed packages which are used heavily in bioinformatics coding. They contain parsers for bioinformatic data file, file format converters, SQL interfaces and other goodies that make a biohacker’s life manageable. Walter Jessen presents a rapid-fire no-nonsense review of Open Source Programming with Bio* Libraries on Expressing Scientific Insight. Finally, if you would like to do everything wrong, Manuel Corpas presents 10 Sarcastic Rules on How to Be a Bioinformatician posted at Manuel Corpas’ Blog.

Databases

Morgan Langille talks about BioTorrents – a file sharing resource for scientists posted at his blog Beta Science. My take on BioTorrents is that it is a cool idea, but as most institutes block BitTorrent along with other peer-to-peer sharing utilities, I doubt there is a critical mass of feeders to make BioTorrents viable. Things can change though: institutes might decide to set up dedicated servers to Torrent scientific data, just like there are legitimate Torrent servers for Linux distros. George presents Bio-graphics, BioSQL and Rails part 1 posted at Biorelated. He talks about how to quickly add graphics support to a bioinformatics database rails application.

Brad Chapman’s Blue Collar Bioinformatics is a treasure-trove of useful bioinformatics methods. Brad is very thorough in his writing, and he covers a wide variety of topics. I particularly enjoyed reading about his adventures at the biohackathon 2010 in Tokyo, and the resulting Python query interface to BioGateway SPARQL endpoint and InterMine.

Genomics

Nick Loman from Pathogens: Genes and Genomes gives some excellent tips for de-novo genome assembly. He also gives the necessary scripts,which are great companions to Velvet, the popular short read assembler. Luke Jostins writes about AGBT: Speculating on Third Gen Tech posted at Genetic Inference, “An investigation into what data from various third generation sequencing technologies may look like.” SM presents Resources for Exome sequencing annotation posted at Organizing the Strands of Curiosity.

Structural biology

Sean Seaver talks about the retraction of several protein structure papers published by one group at the University of Alabama, Birmingham. Structuregate was reported both in the media and in the blogosphere. Sean walks us through how it might have been done, and how structural bioinformatics techniques found out the wrong structures in Origin and Orientation posted at P212121. Maria Hodges talks about how difficult it is to explain structural genomics to the man in the pub. Menachem Fromer presents Tradeoff between stability and multispecificity in the design of promiscuous proteins. Promiscuous proteins are proteins which bind different partners (ligands, or other proteins). However, the more partners they are able to bind, the less stable they are, as shown in a series of simulated evolution studies, summarized at Nir London’s Macromolecular Modeling Blog. OK, promiscuity and and a pub. There must be a joke somewhere there.

Credit: Iddo Friedberg & 3D chem for the Anthrax toxin lethal factor image

A common lament among bloggers and other enthusiastic adopters of Web 2.0 technology is the lack of mainstream uptake of these tools by active scientists. A recent report from University of California Berkeley confirmed this: “The advice given to pre-tenure scholars was consistent across all fields: focus on publishing in the right venues and avoid spending too much time on public engagement, committee work, writing op-ed pieces, developing websites, blogging, and other non-traditional forms of electronic dissemination (including online course activities)“. Maria Hodges argues that Web 2.0 thrives where journals don’t, and that the NMR community might be the first to reach the tipping point, where your career is harmed by not contributing. She talks of two wikis used by the NMR community. It is a small community, which has a need for sharing methods that are generally not publishable in peer-reviewed journals. The wiki venue makes for an ideal dissemination method for this community. On the subject of data sharing, and how it can backfire: here is an interesting connection between the history of the PDB, and the email affair known as ‘climategate’.

Some interesting events cropped up recently. The Marco Island Advances in Genome Biology and Technology meeting was heavily tweeted and blogged about.  Pacific Biosciences unveiled their third generation sequencer. Ostensibly, it can sequence reads of 20,000 length, but the fraction of actual long reads in a run, and their quality is still a bit hazy. The most interested to me is the Ion Torrent. Being rather low on budget, this seems like the family budget car of high throughput sequencing: cheap, reliable, and does not offer more than I really need. $50,000 for a sequencer with $500 runs with 160MB/hr? Nice. Genetic Inference has a great summary of the various technologies presented.

Overall, we are starting to see a divergence in sequencing technologies, as each tech concentrates on having clearly defined advantages and potential applications that differ from all others. This means that the scientists themselves can more closely tailor their choice of tech to fit their situation. Are you a small lab that needs 10 high-quality genomes on a budget? Go to Complete. Want a cheap, fast machine for library validation? Use Ion Torrent. Setting up a pipeline for sequencing thousands of genomes? Go Illumina.

The review article on metagenomics I recently published in PLoS Computational Biology (yeah, yeah, shameless plug) already starts to feels somewhat outdated on the sequencing technology front.

Carnival of Evolution #21 the superstar edition is up: check it out. It’s a nice and detailed one,. Some posts I liked included talking about how human fingers evolved, and why it is important to consult evolutionary biologists when making decision about conservation.

An interesting email I got yesterday: PubGet, a search engine for PDFs of scientific articles, is no linked to PLoS. PubGet is a very useful service that gets  you the article PDF immediately, without going through he usual clickeroo via Google,  pubmed, publisher’s gateway, journal gateway and then squinting along the sidebar to find the PDF link. Nice to see that these two are teaming up.

Finally, two reminders. First, Ada Lovelace day, a blogging day celebrating the achievements of women in science and technology is coming up, March 24. Go ahead, pledge and blog! Second, the Byte Size Biology will be hosting a Carnival of Bioinformatics. Quite a few posts have been submitted already, please submit yours, deadline: March 9.

Haiku:

A finer book of

Blog posts the world has not seen

Buy: you won’t regret

The fine print: one of my posts is published in this anthology

Byte Size Biology will be hosting the first edition of the bioinformatics blog carnival. All you bioinformatics bloggers, submit your entries by Mar 9, 2010 23:59:03  EST. Note the 3 second extension I have already given. There will be no more deadline extensions, I’ve been generous enough as it is. The carnival will be posted here by March 15, 2010.

Any blog posts that have to do with the computational aspects of: genomics, nextgen sequencing, sequence analysis, gene expression, systems biology, ontologies, databases, structural biology, metagenomics, phylogenetics, function prediction and I probably forgot a few other categories so don’t hold it against me, just submit. Early and often. Your own posts and others that you liked. Nothing too old please, 1/1/2009 and later. I reserve the right to be a less-than-benevolent dictator and screen out posts. This applies especially to commercial plugs with no other merits.

Please retweet, reblog, rebuzz and remember:  submit to the bioinformatics blog carnival!

If you have a cool logo for this carnival, email bioinfo.blog.carnival AT gmail.com OhOne and OhToo will pick the winning logo to be displayed on the carnival. Likewise, if you would like to host the next edition, let me know. Do not submit posts by email, only via blogcarnival.com.

Happy carny-ing.

A  small spike on my blog traffic yesterday led me to look for the source via Google Analytics. (If you are a blogger, you should really use this tool, lots of useful traffic information.) Seems like most of the traffic came from the page of a high school science teacher at Badin High School in Hamilton, OH. Apparently the students were to be quizzed today on two of my posts about endosymbiosis (and one from 80Beats; I’m in good company.) So they were very busy Sunday. It’s encouraging to know that some of my posts are accessible enough for high school science. Finally, quite a few Miami students come from Hamilton (we’re close). So I might see some of them next year.

Muahahaha!

My post The Incredible Shrinking Genome was selected for publication in Open Laboratory 2009. The Open Laboratory books are anthologies of 52 posts from various science blogs selected annually by a panel of judges . This year the judges waded through 470 740 nominations (thanks for catching this Bora), so it is great to be selected! How on Earth did they go through 740 posts?

You must buy the book once it’s out, office and home copies. Don’t forget your spouse, lover, friends, colleagues, children and pet hamster, for they will all be deeply offended if you do not get them a copy of Open Laboratory 2009, which may have serious ramifications.  I will link to the book once it is out, in a month or so. In the meantime, you should seriously  consider purchasing the 2008, 2007 and 2006 editions.

In no particular order or context. No personal stuff and by no means a complete list:

Wordpress (like, duh).

Wikipedia (default for looking up new stuff)

Wikis in general (great lab management tool. Don’t need LIMS)

Open Access Publishing and Creative Commons licensing.

FLOSS licensing (90% of the software I use, and 100% of what I write)

Science Bloggers (too numerous to link)

Science tweeters and FriendFeeders (too numerous to link. That’s how I keep up with things)

BLAST (Sometimes it feels like bioinformatics is should be renamed to blastology)

LaTeX (Wrote my dissertation in LaTeX, and never looked back)

OpenOffice.org (because not everyone uses LaTeX).

CiteULike (Keeping my reference library up to date and in good order)

Delicious (Keeping my bookmarks up to date and in good order)

Gmail (because finding that document you sent me a month ago would be impossible otherwise)

Google Scholar (For standing on the toes of Hobbits. Or something like that)

GIS (for blogging and making class slides)

Vim (because emacs blows)

Python (ease & power)

Biopython (OK, conflict of interest here, since I contributed a bit)

Friendly colleagues (They certainly are!)

Good students (gotta make my lab page).

Goulash for dinner. Can’t stand oven Turkey.

Music. Especially the latest song that is going around in my head:

So… yours truly, EssOh, OhOne and OhToo are relocating from San Diego, CA to Oxford, OH where I will be starting a lab at the Microbiology department of MUOhio. Therefore, Byte Size Biology is going on the road. Over the next 10 days or so this space will be filled as much as I can with pictures, road trip trivia, travel music, cheap motel & burger joint reviews. Fascinating stuff, so come back for more. Also, tune in to http://twitter.com/iddux for real-time updates because I don’t know how much I will be able to write after a day of driving (or whether the motel will have a wifi).

Right now, the movers are late, which gives us a bit of a much needed break after the hectic packing over the last few days.  Finishing up my coffee at Starbucks, and going to dump some more trash.

Intelligent Systems in Molecular Biology (ISMB) is a large international gathering of  computational biologists, mostly from the bioinformatics side: genomics, structural bioinformatics, computational genomics, etc. This year there is a friendfeed room for microblogging ISMB 2009. So if you are not in Stockholm, or also if you are, look it up. Most of the microbloggers also have their own blogs, and recap posts on those will be forthcoming (I hope).

My take on microblogging is that it is a nice public note taking mechancism, but going back to recap and provide a deeper analysis of the session one has attended is probably more useful in the long run. Now that I said it, I would probably have to do it. Watch this space.

eMusic, a subscription-based indie music estore has hiked its prices and concurrently signed a deal with Sony BMG to sell their back catalog. What’s wrong with this? Well, a lot. Read my previous post for details. It seems like the reaction on the intertubes has been less than joyful, with phrases like “corporate sellout” and “breach of contract” dominating.

I created an informal poll for eMusic customers, it is ongoing until June 15. The results are below. Yes, I know the many statistic caveats to an Internet-based poll. But if you take the results of this survey together with the bulk of the reactions on eMusic’s message boards, various blogs, and chatter on social networks, it seems that eMusic have a serious problem to fix. If you are an eMusic customer, please take the short poll.

Title:	eMusic Customer Survey Results
Description:	Ongoing poll

Click here and refresh the resulting page to get the most recent numbers.

Harvard University has removed from YouTube the video I embedded  in my Leonardo Da Vinci and the F0-F1 ATPase post, due to copyright concerns. It is a pity. I believe the main sufferer from this step is the lab that actually created this video, and now has one outlet less to publicize its work. One would think that after a projected loss of 30% of their endowment, Harvard would come up with more creative ideas for freely publicizing their researchers’ fine work, not less. (Yeah, I know no one reads my blog, but everyone goes to YouTube, including people who don’t normally read Nature).

Whatever. I hope that the IP admins at the  MRC in Cambridge (UK) have a more advanced view on these matters than their concurrents in Cambridge (US), and will keep the following videos up. Here are two F0-F1 ATPase videos from Dr. John E. Walker’s lab. Incidentally, John E. Walker received the 1997 Nobel prize for physiology or medicine for his work on the ATPase enzymatic mechanism. You may find some of these movies on his web page.

The first is a general overview of the F0-F1 in action:

The second shows views from above and then below the F1 domain around the rotating gamma subunit (that’s the blue eccentric stator in the middle):

The third is a group of what appear to be Japanese grad students /postdocs demonstrating the ATPase dance. I have no idea where this came from. I give them a “C-” in dancing, but an “A” in structural biology (to get an A+ they should have tossed tennis balls to represent synthesized ATP):

Shirley Wu has penned a beautiful open letter to Oprah Winfrey explaining why Oprah should not provide a soapbox to Jenny McCarthy. McCarthy is the unofficial spokesperson for the anti-vaccination movement, a dishonorable position at best.  Given yet another podium, more people will listen and take McCarthy’s bad advice, resulting in more deaths and preventable serious illnesses.

Remember this?

Wordle is a toy for creating word clouds from text. Each word’s  size is correlated with its frequency in the input text.  Every three months or so I will generate a Wordle from the RSS feed of this blog, to see whether this blog has any direction, theme change, and just because Wordles are cool. Click on image for full size.

Hypatia, detail from "School of Athens" (1510) by Raphael Sanzio. CC Wikimedia Commons

Hypatia  (b. ~360CE  d. 415CE) was a mathematician, philosopher, astronomer and teacher in Roman Alexandria. She was also quite probably the last librarian of the famous Library of Alexandria. Note that at the time, the definition of Philosophy was much broader, and encompassed what we term today the natural and exact sciences; and yes, she was also a techie. She is credited with inventing the hydrometer, for measuring the specific gravity of liquids.

In a time of political turmoil, she appeared to have supported the secular authority Prefect of Rome, Oresteus against the Pope of Alexandria, Cyril. Eventually, this cost her her life. Socrates Scholasticus (Socrates of Constantinople), a 5th Century Christian Church Historian wrote in Historia Ecclesiastica:

Chapter XV.–Of Hypatia the Female Philosopher.

There was a woman at Alexandria named Hypatia, daughter of the
philosopher Theon, who made such attainments in literature and science,
as to far surpass all the philosophers of her own time. Having
succeeded to the school of Plato and Plotinus, she explained the
principles of philosophy to her auditors, many of whom came from a
distance to receive her instructions. On account of the self-possession
and ease of manner, which she had acquired in consequence of the
cultivation of her mind, she not unfrequently appeared in public in
presence of the magistrates. Neither did she feel abashed in coming to
an assembly of men. For all men on account of her extraordinary dignity
and virtue admired her the more. Yet even she fell a victim to the
political jealousy which at that time prevailed. For as she had
frequent interviews with Orestes, it was calumniously reported among
the Christian populace, that it was she who prevented Orestes from
being reconciled to the bishop. Some of them therefore, hurried away by
a fierce and bigoted zeal, whose ringleader was a reader named Peter,
waylaid her returning home, and dragging her from her carriage, they
took her to the church called Caesareum, where they completely stripped
her, and then murdered her with tiles. After tearing her body in
pieces, they took her mangled limbs to a place called Cinaron, and
there burnt them. This affair brought not the least opprobrium, not
only upon Cyril, but also upon the whole Alexandrian church. And
surely nothing can be farther from the spirit of Christianity than the
allowance of massacres, fights, and transactions of that sort. This
happened in the month of March during Lent, in the fourth year of
Cyril’s episcopate, under the tenth consulate of Honorius, and the
sixth of Theodosius.

Ian Holmes introduced me to Ada Lovelace day. I pledged to blog this day, and here we are. Hypatia was an intelligent, courageous, free-thinking woman who paid dearly for her beliefs, her principles, and if you can read between the lines, her gender.

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, passed out, and left its driver’s license, along with most of its cash on the dresser at some floozy’s room.

Early Bioinformatics Conference

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