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Category Archives: Services

“Startup weekends” in science

News about yet another “startup-weekend-like” event keep hitting me more and more often. They do not always are about creating a company or a product. Sometimes it’s about collaborative coding a game or writing a novel – all in very short time. In many cases it works amazingly well – being so tight on time forces people to be ultra-productive and to be focused only on important parts of the project. I envy people attending such meetings, not necessarily because of possible outcomes, but because of the energetic atmosphere that is present there.

Deepak wrote some time ago about “Bursty work” – idea, that work can be done by distributed teams focused around high value projects, instead of teams gathered around company/startup. That actually made me think if we can join these two ideas in science: to have ultra-productive and distributed team working on time-constrained project.

Lets assume that the average publication in the field of bioinformatics/computational biology takes six months of work of one scientist. It doesn’t really matter if it’s new server, database or protein family annotation. So a team of four people should do the same work in six weeks or faster (why faster? knowledge and skills are not distributed evenly, so someone else may code the necessary script faster than I would do it). If we would increase even further the number of people involved, create a distraction-free environment and prepare enough coffee for everyone, the whole process could be done in a week. Even if the assumptions here are not really correct, I’m pretty sure that quite a number of valuable papers could be done this way in a week.

So what do you think? What about creating a platform that allows for:

  • creating a project that has a clear and appealing outcome (for example publication, or at least manuscript in Nature Precedings)
  • creating a project workspace with all necessary tools (wiki, chat, svn, etc. plus small computational backend for testing)
  • creating a number of roles, that need to be filled by people with certain skills
  • joining the project if the skills match requirements
  • setting an clear deadline (for example, a countdown clock that will forbid to commit changes to the project after certain amount of time, leaving the workspace read-only)

I agree that science takes time, especially the quality science. But on the other hand, I have a feeling that we waste a lot of time learning things by ourselves, instead of learning form others, we waste this time because the outcome is not well defined, and finally we waste time solving everything ourselves instead of bouncing the idea against other people (this is what collaboration is all about). So what about creating an artificial environment that forbids wasting time?

Utopian? Maybe. Naive? Most likely. Worth considering? I hope so. Let me know.

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Jane – Journal/Author Name Estimator

Jane – Journal/Author Name Estimator is a new web based application that can suggest potential reviewers or target journals for a manuscript based on its title and abstract. It was just published by Bioinformatics under Advance Access (but unfortunately it’s not an open access article). I have tested two of my upcoming publications and Jane performed well: I wasn’t surprised by most of predicted names and journal titles. The topic I’m writing about in these papers is rather narrow, so don’t treat it as any performance measure – test it yourself, if you are interested.

Probably I’m not going to use it as authors suggested – I consider this application a helpful literature research tool.

 
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Posted by on January 28, 2008 in bioinformatics, Papers, Research, Services

 

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DNASIS SmartNote – online notebook for bioinformatics analysis

I’ve found recently a video showing new web-based application for scientist. This is DNASIS SmartNote – an online notebook for sequence analysis, project organisation and sharing results, thoughts and data with other users/collaborators.

This service is provided by MiraiBio which belong to Group of Hitachi Software. This company provides instruments and software for biological research.

As soon as I resolve issues with obtaining a working account on the SmartNote (so far I cannot log in), I’ll post more about this service.

 
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Posted by on January 19, 2008 in bioinformatics, Services, Software

 

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Software portability and virtual appliances

Bioinformatics can mean developing new algorithms for biological data analysis. Scientists who code and release the software face often an issue of making the program portable. I see three clear solutions to that issue. First, one can spend a lot of time porting the source to other platforms (plus testing, fixing and yelling at incompatibilities). This is not easy even within the linux OSes (remember broken HMMER binary packages with Debian and Ubuntu?), not to mention porting to OSX or Windows. What can we do? Second solution is to build a web interface around the software. This is extremely popular and makes almost everyone’s life easier. However there are drawbacks: maintenence of the service (it costs money and grant agencies are not willing to spend a dime on it) and batch access requests from some users (there’s always somebody who wants to feed into your software 5 millions sequences or 50 thousands structures). The third solution to the software portability issue can address at least the second of these drawbacks: one can create a virtual machine with a proper enviroment for developed software, and release it together. Yes, release a software together with the whole enviroment. And it’s not that difficult, as it seems.

We face computing clouds, internet companies that do not have a single server, virtual appliances for quick installation of, let’s say, blog server with WordPress, without any knowledge about software requirements. Virtual appliances, this is complete virtual machines, can contain already configured software (most trivial example would be LAMP – Linux, Apache, MySQL and PHP). So far I found only one such appliance for bioinformatics: it’s called DNALinux Virtual Desktop Edition and contains, among others, BLAST, EMBOSS, Pymol, BioPerl and Biopython. Since VMWare server is free (although registration is required), this makes pretty nice alternative for those with Windows machines, as it allows for running windowed linux at a speed of ca. two-thirds of a native system. VMWare software can create a virtual machine out of the working system, but I wouldn’t recommend that as we usually have much more software installed than it’s needed to run our own programs. So creating a virtual appliance for, let’s say, BLAST, would mean installing a fresh copy of our favourite linux under VMWare Server with nothing more than necessary libraries, copy of BLAST executables and possibly a web interface. Voilla. Virtual appliance for BLAST, anybody?

While it may seem a bit of overkill at first, I don’t think it is in the long run. Porting the software to other operating systems is only part of the story – maintenance to keep it working with newer version of the libraries is another. There’s a lot of programs that are not actively maintained for a long time. I have two quick examples where virtual appliance approach would save them from forgetting: PovChem (rendering of molecules, depends on some ancient libraries) or MACAW (it doesn’t work on anything but Mac OS 9, Windows version crashes the system). OK, MACAW may be not fair, as we face here legal issues with the operating system, but I believe any heavy software user already didn’t count how many times hadn’t tried some well-thought software because of its requirements.

Have a look and try. I’m already running two operating systems (good bye dual-boot) and this is definitely a future for our desktops with already too much processing power. But honestly I dream about a day, when all possible bioinformatics algorithms and biological data will be available at some computing cloud and running Taverna will be a good alternative to all day data munging.

 

 
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Posted by on November 27, 2007 in bioinformatics, Services, Software

 

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Biology Image Library – scientific stock photography?

(via The Biotech Weblog) BioMed Central has launched the Biology Image Library – online collection of scientifically interesting and meaningful images across biology and biomedicine.

Most of the images at BIL are available free of charge for non-commercial purposes (like teaching), but buying commercial-use rights is also possible. I don’t really agree that the library is aimed at students (teachers, lecturers – maybe), since personal subscriptions are $293 per annum and I could imagine that institute subscriptions are not cheaper. UPDATE: See comments below. To me a corporate client is a main target of this initiative, but I may agree that relatively high subscription rates may be dictated by the nature of the images – most of them come from experiments (almost no computer generated illustrations).

Microstock photography sites hold quite a lot of science-related images, however their scientific value is very often zero (as an example, search for DNA). It is overall nice idea to have a scientific equivalent of a microstock, but I would rather leave the subscriptions out and release low quality (for web/computer screen use) material under non-commercial Creative Commons license.

clipped from www.biologyimagelibrary.com

What is the Biology Image Library?

The library is a collection of images, illustrations, movies and animations that are useful for research and education. It is also a new, easy way to share your work with others without losing any rights to it or limiting how you use it in the future.

Who publishes the library?

The library is published by BioMed Central, an independent publishing house that offers a wide variety of journals and other online services. BioMed Central is committed to providing immediate open access to peer-reviewed biomedical research. We also publish a number of “value-added” subscription databases and information services, of which the Biology Image Library is an example. Please see www.biomedcentral.com for more information about our activities.

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Posted by on October 22, 2007 in Clipped, open-science, Services

 

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