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Monthly Archives: January 2009

Microblogging in PLoS

I don’t usually repost news, as my FriendFeed stream (also available from the sidebar of this blog) is a more efficient way to let you know about interesting things, but this one deserves a special mention. Recent coverage of ISMB 2008 conference over at FriendFeed ended up as a publication in PLoS Computational Biology:

Saunders, N., Beltrão, P., Jensen, LJ, Jurczak, D., Krause, R., Kuhn, M. and Wu, S. (2009).
Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput Biol 5(1): e1000263
doi:10.1371/journal.pcbi.1000263

This is very exciting, but it also has some interesting implications. Of course it means that more and more people will participate in our community and finally BioGang projects will start to take off (hopefully), but I think also about something else. Do you remember Neil’s post about why you should have online presence? I think there’s one more thing to add to this list. Authors of this publication and lots of others scientists over at FriendFeed will sooner or later climb to to a PI-equivalent positions, where they can decide about hiring somebody. And strong online presence will be for them an important asset in CV. Much more important than you’d think today ;).

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Posted by Pawel Szczesny on January 30, 2009 in Community

Tags: bioinformatics, FriendFeed, microblogging, PLoS Computational Biology, Public Library of Science

Timestamped FriendFeed activity – really public “profile”

29 Jan

Accidentaly, I have found a simple way for obtaining a time stamp for each entry and comment any person with publicly available lifestream makes on FriendFeed (except “Likes”, which do not seem to be timestamped at all). Activity of semi-randomly choosen person during the day (summarized over couple of weeks (!)) is shown below:

FriendFeed usage during 24 hours, summarized over couple of days.

While relation between AM and PM periods is correct, time-zone is manually shifted, so it’s more difficult to guess who’s this activity is (but it’s not Robert Scoble if you want to ask). What does it tell? Basically, this person does not close FriendFeed window for the most of the day. Additionally, there’s a period of the day in which “catching-up” has place. Nothing interesting so far? Original data has much more details. It is possible for example to collect information when during the day particular person usually watches videos on YouTube. Guess – is that during working hours? 🙂

Ability to get that data for couple of weeks back without any trouble (I didn’t need to track this person’s activity for such period) was kind of disturbing. I knew it’s very simple to start tracking my habits, but I wasn’t aware of the fact that it’s also easy to see what I was doing over the last three weeks. Do you think it makes a difference?

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Posted by Pawel Szczesny on January 29, 2009 in Comments, Visualization

Tags: activity tracking, Blog, FriendFeed, RSS

Science & Art: what language do you use?

27 Jan

: Image by cr8it via Flickr

I’ve just realized where is the important difference between artists and scientists – and probably the biggest challenge of the merging or communicating between these two areas. When we do research, we tend to think in words. When we paint, we tend to think in colors. When we compose, we tend to think in sounds. Our right hemisphere thinks in colors, images, feelings or sounds, while the left thinks almost exclusively in words/in symbols. This is of course an over-generalization, but still I think it’s very important point when discussing relations between science and art. Putting right hemisphere experience into words is so difficult task, that most of such attempts sounds like gibberish. Have you watched TED talk “My stroke of insight”? Jill Bolte Taylor shared her first person observations from the stroke, which turned off her left (logical and analytical) hemisphere. While she did great job (also of not going too much into details), still some commenters were complaining about scientific quality of these observations (or that she sounded like she were on drugs, which is by the way not a coincidence).

If that sound too abstract to you, consider history of discovery of benzene. Kekulé had a day dream of snake seizing its own tail – and interpreted it correctly. And I believe this is not a single example, where solution to a scientific problem presents itself to a researcher in some non-linguistic form (or rather right hemisphere sends solution to left hemisphere). However, such stories are rare for a couple of reasons: we are not usually aware of the fact that “artistic” hemisphere can “solve” scientific problems, we lack skills to identify and translate such messages, and finally it seems unprofessional to admit that we had a “vision” that led to a successful solution.

I’m not sure about correctness of these speculations. It has been quite difficult to get to that point, exactly because of limits of linguistic description of the Art (I rarely can stand an artist’s statement), so it’s likely I’ve made some mistakes on the way. Therefore I would appreciate any help along the way.

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Posted by Pawel Szczesny on January 27, 2009 in Science and Art, Visualization

Tags: ART, Jill Bolte Taylor, Language, Neurological Disorders, science, Science&Art, TED, Visual arts

Database query and ranked results

22 Jan

: Image via Wikipedia

Already some time ago I’ve read a piece by Marcelo Calbucci: Is it a database or a search engine?. While it deals with search information within a real estate database, I think his comments are applicable in the many areas of life sciences.

In short, Marcelo points out that people miss a lot of interesting entries while looking for a house, because of inflexibility of the query; number of bedrooms, price, distance from some point – these are all set. However, users are flexible and in such case need rather a search engine that gives them close enough answer or allows to specify weight to each filter.

In life sciences we do search for similarities and analogies all the time. Sometimes it’s direct comparison of sequences, on other occasion is high-level meta-comparison between two systems. And while we have various (statistical) metrics of similarities and they sometimes become a part of a database designs, interfaces of biological databases don’t allow to rank query results according to these metrics. For example I can easily find all human proteins related to disease X or disease Y or disease Z, although I cannot specify that I want proteins related to Z AND Y first on the list. Other example would be searching PubMed – I can look for articles related to “synthetic biology”, but I have no way to specify, that I want papers by James Collins from HHMI AND articles related to these papers to be first on the list. I guess it is possible to obtain such results without going through the whole list, but I doubt the method will be very simple. Filtering still seems to be neglected aspect of database design in life sciences.

My dream biological search engine would have a series of sliders (or ideally, I would like to have a device with series of mechanical knobs attached to the computer) and would allow me to dynamically change weights of various aspects of the query and see immediately how it affects the results. It would be something resembling interactivity of Gapminder World, but on dynamically generated data. Technology and proof of concept seems to be there, but I guess we need to wait quite a few years before this approach will be adopted within life sciences.

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Posted by Pawel Szczesny on January 22, 2009 in bioinformatics, Data mining, Software

Tags: bioinformatics, Database, PubMed, Search, Web search engine

Collanos Workplace and scientific collaboration

15 Jan

One of my workspaces in Collanos

For some time already I was looking for a tool that would eliminate a need for sending files back and forth between people collaborating on a the same project. While I’m perfectly aware of various solutions such as wikis, version control systems or online office suites, I didn’t feel like I could convince my collaborators to use any of these. One of the reasons is always a feeling of insecurity when using publicly hosted platform (BTW, this is not that uncommon among scientists – I know at least one scientific institution in Western Europe that explicitly forbids using Google apps, especially Gmail for work-related stuff, because of Google’s privacy policy). The other reason was that such solutions are not the best choice when working on binary files (most of my projects do not involve collaborative programming). When I stumbled across Collanos Workplace, which offers peer-to-peer synchronization (although without revision control), instead of a central-server based, I’ve decided to give it a try. For the last couple of weeks I’ve been using Collanos to collaborate on one relatively simple project and the experience was quite positive.

At first, I thought that Collanos may serve mainly as a tool for secure peer-to-peer files sharing with an information who changed what etc. It turned out that this is a capable project management application, that has a chat and discussion panel, one can post notes, links add tasks and assign them to team members. Files are stored is a separate directory – after one adds a file to Collanos, it should be opened from the application, not from original folder. This seemed a mistake in design at first, but I appreciated it very quickly. Synchronization of project directory would mean sharing all of its contents and that can be sometimes in the range of many GBs. From time to time some bug appeared here or there, but overall it worked as expected. Peer-to-peer sharing means that both people have to be online for synchronization, but so far situation that I switched computer off before a person could download my changes happened only once and it was during a weekend.

As a side note, it’s nice to see that Eclipse becomes an application platform for quite a number of programs. See for example this list of Eclipse-based software.

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Posted by Pawel Szczesny on January 15, 2009 in Research skills, Software

Tags: Google apps, Office suite, Peer-to-peer, Project management

Science and art. New theme for the new year.

11 Jan

: Image via Wikipedia

In 2007 this blog was mainly scientific. Last year I’ve explored possibilities of being a freelance scientist. As I’ve announced earlier on Twitter, theme for this year will be science and art. And I should already explain: I’m not going to write about such extraordinary artistic endeavours like creating music from DNA/protein sequence, try to convince you that science is beautiful or state that my pictures of molecules are the true art. I’m more interested to see if there’s anything I can learn from The Art, its history and its approach. While I’m not yet sure what I will end up writing about, here are two topics I may start with to see in which direction this theme unfolds.

Holistic approach to science

This is something I was thinking about for a while. I didn’t come up with anything interesting, but I think it’s worth exploring further. Some first ideas were coming from reading Wikipedia entry about lateralization of brain functions or Steve Brenner’s comments about “middle-out approach” (as opposed to top-bottom or bottom-up). I’ve also found peculiar Mihaly Csikszentmihalyi‘s answer to Edge 2009 question, where he wrote about “The end of analytic science”. Very recently I’ve also found interesting interview with Daniel Tammet, autistic savant, who explains his theory of exceptional creativity coming from “hyper-connectivity” of distinct brain regions. I have no yet idea whether there’s anything practical to find in such theories, but their exploration will be appealing enough.

Dashboard design for scientific data

This is something more practical, although again I expect to get no points for that topic. Information dashboard is a very cool concept rarely used in life sciences. One of the best known examples in bioinformatics may be InterPro domain page (here’s example entry on pore-forming lobe of aerolysins) – almost everything is on the single page, it has some nice graphical overviews of particular features (like species distribution), etc. It’s not the prettiest dashboard around, but at least you don’t need to click anywhere to have an overview of stored information (compare it to PFAM approach to similar domain). I hope to learn what makes a great dashboard, experiment a little and see if the result is worth the effort.

Other topics

I still will be blogging about bioinformatics, visualizations and open science – that stays in place. Especially the last topic is something I expect to write about quite a lot – my feeling is that this year will bring couple of interesting events in this area (and I hope to initiate some of them). So if you don’t like the “science and art” theme, I think I will give you some other reasons to visit this blog once in a while.

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Posted by Pawel Szczesny on January 11, 2009 in bioinformatics