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Proposal for Science 2.0 lectures

I’ve just submitted a proposal for three lectures about different aspect of Science 2.0. Target audience are PhD-students. Below you can find a brief overview. Probably the details will change a bit when I start to prepare the lectures (for example I’m aware that Etherpad is on its way out), but nevertheless you are very welcome to comment and suggest different approach.

Science 2.0 – practical aspects of the internet revolution

Part 1 – communication, collaboration, visibility

New communications channels (blogs, microblogs, aggregators, virtual conferences ans poster sessions) and examples of successful applying in science. New roles of blogs, Research Blogging initiative. Wikis, Etherpad and Google Documents/Wave – platforms for document co-writing. Collaboration for programmers, Git. Visibility and recognition in the internets: StackOverflow and ResearcherID.

Part 2 – practical open science

Spectrum of openness in science. Community annotation of genes/proteins/structures and why these aren’t so successful. Crowdsourcing and citizen-science. Overview of open data repositories, focusing on open data coming from pharma industry. Mechanisms of Open Access and Open Notebook Science. Current discussions on intellectual property – what’s not protected and what’s not licensable?

Part 3 – searching for information and literature management

Information overflow – myth or fact? Searching for information – differences between PubMed and Google Scholar. Semantic analysis of abstracts based on GoPubMed and NovoSeek. Targeted text-mining tools. Literature management: online (Connotea, CiteULike) and desktop (Zotero, Mendeley) approaches. Alternatives for EndNote. Automated or not – literature recommendations.

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Posted by on December 7, 2009 in Community

 

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(Do not) Beat ideas half to death

This is short post/note to self – to see if the way I think about science today will change in couple of years. Its enigmatic title comes from Stu Jenks, one of my favourite photographers. He wrote in the introduction to his works:

I’ve been doing a series of spirals. You know how it is with us artists. We take one idea, and then beat it half to death.

If we substitute “artists” with “scientists” it still sounds true. This is efficient (in modern terms of scientific productivity) way of doing research, but probably not always the best one. While I know that many breakthrough discoveries in science were results of years of hard work, not all of them required fifteen years to establish a procedure only. So, the question is if rapid switching between fields (every few years or so) is a good idea? It probably depends. Ask me in a few years how it works in my case.

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Posted by on February 17, 2009 in Comments

 

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Science & Art: what language do you use?

TED 08
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 on January 27, 2009 in Science and Art, Visualization

 

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Bug tracking systems in science

I’m not going to describe painful process of correcting entries in biological databases or errors in publications when one is not the author – we all know how difficult and unrewarding it is. All major databases contain wrong entries – I see misannotated (or nonexistent) genes in Genbank, artificial domains in PFAM or poorly solved structures in PDB. It’s even worse in publications, where across the whole spectrum of journals I see errors which in theory shouldn’t slip through peer review (this includes such prominent publishers like NPG).

One of the best idea I heard that addressed this issue was to build a bug tracking system (I would like to give credit to the author, but I cannot find the source; wasn’t that one of biobloggers?). It’s simple and efficient. Something is wrong? Fill a bug report. It would be linking to the original entry, would be available for aggregation (for example to track report’s author activity), and possibly could be closed by somebody else than database maintainers or authors if it’s wrong. Because it would be external to all databases, maybe it could grow to provide “community corrected” versions of these databases?

What do you think? How useful such system could be?

 
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Posted by on April 18, 2008 in Comments, Community, Software

 

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Freelancing science – today and tomorrow

In response to recent Neil’s comment and questions that repeat in emails, I’ve decided to describe in little more detail my status as a freelancing scientist. However keep in mind that I have no idea about such arrangement outside of Poland, so it is likely that some things may look different in other countries.

First of all, I need to explain my unemployment: I have a academic affiliation, but I’m not formally employed and I don’t get a salary, but I do get non-financial support and I am able to apply for grants, access free software and journals the institute is subscribing. I was told that’s similar to a tenure in US – you get your office and lab space, but little or no salary. But the difference would be that instead of applying for an independent position, you just take it :).

My income comes from grants and subcontracting other people projects. As a bioinformatician, I don’t have huge needs, so grants I applied for were pretty cheap compared to grants for experimental biology. However, it can take as long as half a year to a year to get an initial cash flow – it’s all about the time between a call and awarding the grant. Many times your degree doesn’t matter when applying for a grant, especially if you are not a principal investigator in the application. I still do not have a PhD degree, and while I hope to get one sometime this year (finally), I’m not pushing this that much.

Instead of carefully listing all good and bad sides of my freelancing status (or explaining reasons why I did such move) I will try to answer a question which I also hear often, which is: where is this heading?

In my probably skewed view of science to do things which are very novel and very cool one needs to be or a recognized genius, or a big shot in particular field. Otherwise, it’s hard to get enough money to fund one’s completely crazy projects. I’m neither a genius nor a big shot but I have bunch of ideas I consider cool and which I’d like to get funded. It looks like for that I need to step out of academic money-flow system, and apply for funding to people who are less conservative and who can take a risk of supporting non-established ideas (Deepak, thank you for the inspiration). And that’s the plan: leave academic (and competitive) funding system and shift to an outcome oriented one, similar in essence to a startup. And instead of waiting 15 years to get recognition in academia, I hope to get my stuff running within the next few years.

One can argue that it’s risky and one could achieve similar outcome following traditional academic career path within a similar time. Probably that’s true – all of the things I’ve just written are not really supported by long term evidence. But on the other hand, even if the whole idea doesn’t make sense at all, compared to my colleagues, I am having much more fun…

 
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Posted by on April 5, 2008 in Career

 

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