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Monthly Archives: July 2008

FriendFeed: where the conversation happens

The start of this post (see the image above) may be a good reason for many people for not to join FriendFeed :) . It shows what happened to number of visitors to this blog after I joined FF – it had dropped by half (actual numbers aren’t relevant, graph shows monthly statistics). The reason is pretty obvious for any long-time blogger – no posts, no visitors. I don’t post as often as before for a good reason – sharing news, interesting links and the whole conversation around these happens on the FriendFeed. While I didn’t set up a dream system I wanted to (see my comment on previous post on the FF), I don’t have any issues with so-called “information overload“. Actually, I don’t believe in any information overload – we are just pretty bad at managing incoming information – but that’s a story for another post.

Rooms are neat feature of FriendFeed – they act a filter and keep the conversation focused. Instead of looking at a stream of titles ranging from linux hacks, through hardcore programming stuff and other bioinformatics-related topics, up to cancer research and science philosophy, I can just go into one of the rooms and see only items related to a particular topic. Yesterday Deepak wrote on the new rooms at FF (for Python, Ruby and R for Bioinformatics) that were created by people from life-science community. There is also a room for Science 2.0 and Open Science, DIYBiology and even a room which collects links to a must-read material – BioGang classics (since I started this post, Ricardo had created OpenWetWare FriendFeed room).

Rooms help in keeping the flow of links under control, but the conversation is the key point of using FriendFeed. Almost every single item posted into The-Life-Scientists room generates comments, sometimes turning into pretty long discussion. Because FF aggregates Twitter updates, majority of “Dear Lazyweb” Twitter requests result in FriendFeed based conversations. And there’s more and more people participating (The Life Scientists room has over 200 members). As usual, there’s a catch – focus and depth are not good sides of FF comments (for example, compare reaction to the recently posted very nice essay by Michael Nielsen on The Future of Science: number of comments on his blog and on the FF are comparable, although discussion/arguing with the essay points happened mostly on the blog). But that’s not a problem – it’s just a result of a speed with which items appear and disappear on the FriendFeed (some of you have seen that tracking real-time stream from concurrent sessions on the recent ISMB conference).

Even such shallow and quick interactions with people on the FriendFeed generate some level of trust, and that I think will lead to couple of interesting things:

  • more people will try how does the online collaboration work (for example, in reflection after recent Cameron’s talk Brian Kelly from UKOLN wants to write his article online)
  • PI-level scientists will join FF to participate in the discussion (we see that already, although so far there’s only very few of them)
  • there will be serious articles why FriendFeed, Twitter and online collaboration are bad for scientists and how these can break their academic career, in similar way as there were for blogs (see recent Pedro’s post)
  • we will see (and read, since it’s going to be open-access) first peer-reviewed publication from an idea that originated at FF/Twitter

Is FriendFeed going to be a hub for science? I don’t really think so. At the time, when mainstream science will pick up FriendFeed I think we are going to be already somewhere else, because there will be more interesting and more useful platforms for scientific collaborations (like for example cyn.in – looks promising, although it’s not yet optimized product). But the time spent at FF will give us an advantage: connections, collaborations, wide spectrum of information and advice from smart people.

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Posted by on July 28, 2008 in Comments, Community

 

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Growing in open source business model

cleanedImage by *w* via Flickr

Last couple of months I’ve been quite busy with writing PhD thesis and few other projects, but also I was trying to start an open project balancing between academia and industry. This balance sounds like an opportunity, but in fact it was an issue instead. The issue wasn’t in the money – I was lucky to find people willing to help me in getting funding. The issue was rather in what I need to give away in exchange for the money – openness, control over the project or all intellectual property rights. Being already established scientist or a business person would solve such issues immediately, but I am still PhD student, so I need to face it. And while I have still plenty of people to talk to (I think it will take another month or two), that left me thinking about career on the border between industry and academia.

On both sides, in academia and industry, career path (and I’m not talking here only about having a job, but also about starting a business by yourself) is somehow clear and one can get a significant help along the way, but I haven’t found such clear path on the border between these two. Open source business model seems to work well mostly for very established players (such as Apache or RedHat) – growing in such model looks much more difficult than on either of sides. Probably Antony Williams from ChemSpider (who was one of the people that inspired and encouraged me to follow this path) would say much more in here, especially how easy (is not) to get a financial support for working on a project like ChemSpider.

I don’t think about working in one or the other environment anymore. Being freelancing scientist has a lot of good sides and growing wouldn’t be an issue (for example I have enough collaborations and ideas to cover financially next 3-4 years from grants; publications would follow). But, as I wrote before,some of the projects I’d love to work on are unlikely to be funded in academic system. On the other hand, openness is too important for me to give it away, so only a merger of these two sounds interesting. There are few examples of successful merging industry and academia, but they all seem to operate on different principles, compared to my recent attempts. Craig Venter’s model was as far as I know most of the time double-sided – he had a non-profit search unit and a company that commercialized its discoveries. Pretty similar has also David E. Shaw. So I have started to wonder if sticking to borderline is actually the very best idea. Being involved on two fronts at the same time sounds pretty overwhelming, but so far these are the only examples when this whole idea seems to work. Are you aware of any others?

My other hope is that new ways of growing on the borderline will very soon emerge. There’s quite a lot happening right now on the front of supporting innovations (including open models), so maybe over there I will find my niche. We’ll see.

(The image above is not my desk. While I work in a home office, mine doesn’t look so clean.)

Further reading:

A microfunding system for research and innovation.

Pharma looks at new ways of innovate.

Discussion around business model around Open Data is building up.

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Posted by on July 21, 2008 in Career, Comments, Research

 

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Bioinformatics Career Survey – two weeks left

If you haven’t filled the survey yet, please spend few minutes to do so over at Bioinformatics Zen. There are only two weeks left.

 
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Posted by on July 21, 2008 in bioinformatics

 

Configuring Torque and InterProScan

Image via Wikipedia

If by the chance, you want to use InterProScan with Torque Resource Manager (queueing system based on PBS project) it doesn’t work by default (it’s tested with LSF, configuration files are supplied for original PBS and Sun Grid Engine). Fortunately there are two small changes needed in the InterProScan config files to make it work. First, during iprscan configuration, choose PBS54 as your queueing system. Then, in the file pbs54.conf (IPRSCANHOME/conf) remove “-d” switch from following two lines:

asyncsub=qsub [%optqueue][%optresource] -d -o /dev/null -e /dev/null "[%toolcmd]"
syncsub=qsub [%optqueue][%optresource] -d -o /dev/null -e /dev/null -I "[%toolcmd"]

Assumming that Torque binaries are available in the global PATH (qsub, qdel etc., on my machine they sit under /usr/local/bin), change in default shell in the enviroment file pbs54env.sh – from #!/bin/sh to #!/bin/bash. Also, you can add another directories to the PATH in that file (I didn’t). Voilla. InterProScan jobs are now queued.

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Posted by on July 10, 2008 in bioinformatics, Software

 

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Human genobiome and disease risk assesment

Schematic diagram of the life cycle of {{w|Esc...Image via Wikipedia

I’ve recently attended a talk on the advancements of human metagenomics projects. As the speaker admitted, the whole field is a researchers’ gold mine – almost all they find is new and interesting. There were couple of interesting points – mainly concerning how limited our knowledge about things in here is. For example, there was a unconfirmed feeling among microbiologists that in fact all modern microbiology is nothing more than biology of E. coli and relatives. Now we know that for sure – number of known to us microbial species is estimated at 0.5% of all existing microbial species. Also, I heard a nice story about polish doctor who described in 19th century Helicobacter pylori and its role in gastric diseases (there was a Nobel prize for that in 2005), wrote a book and then trashed the whole thing because he couldn’t grow the bacteria in a pure culture. Another important issue was amount of data and lack of new ways of handling them.

But the most interesting for me was a connection between human microbiome and diseases. Or rather a possibility of such connection. I am not aware of any single case when composition of human microbiome have been proven to influence chance of getting ill and I don’t think there will be a lots of such correlations found soon. My impression is that correlations are to be found when we have both, a complete human genome and a complete metagenome of all that lives on particular person – a human genobiome, as I’ve called it (BTW, word “genobiome” is not present in Google – is there a better word for that?). And I believe that getting the first full human genobiome will be the achievement compared to sequencing human genome for the first time. Not because of technical difficulties – because of the all discoveries that need to be made to make it happen. For example, human gut of all people carries a species doing some sulfur reaction – but  its population is only up to few thousands cells. How many such cases are we have in our organisms? That is very good question. The field is brand new, and possibilities of speculations are endless.

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Posted by on July 6, 2008 in bioinformatics, Research

 

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