Category Archives: Community

One year of blogging – plans for ten years

Ethos Roundtable at Bob Doyle's Home - July 18...Image by Pathfinder Linden via Flickr

Following BioBarCamp I missed one year anniversary of this blog. With sixty something posts I cannot say I’m very productive blogger, but I didn’t aim at being one, as probably all other science-types. My goal was to be engaged in the conversation and I have reached it much faster than I expected. I got lots of help and encouragement from people I wouldn’t even dear to email a year ago. I know much more than I did on things outside of my research area. While it sounds all pathetic, advantages of being part of this community are hard to overestimate – I wrote about it couple of times already (and Neils did a great job summarizing why you should have a web presence).

Where is “Freelancing science” heading? That’s a question I asked myself pretty often during last 12 months. At first, I just blogged about interesting stuff around bioinformatics. Then I made a jump into freelancing as scientists (and this experiment goes pretty well). Statistics on keywords people are using to find this blog clearly show that there’s some interest within bioinformatics community in following this path. But the idea for this blog I have right now is not about freelancing anymore. Or rather it’s about freelancing on the next level, because today I think about starting a non-profit institute.

I believe that small research groups formed as a non-profit organizations will have enourmous impact on science within next ten, twenty years (more about it in upcoming post about the future of scientists). In spirit of freelancing they will jump from one project to another (see Deepak’s post about bursty work and follow-ups), developing solutions and making discoveries much faster (or cheaper) than it is possible in beaurocratic environment. We do have tools for effective collaboration online, we have new generation scientists that do not feel attached to academic system and we have science which starts to evolve about undestanding data, not performing experiments. Is it time to try such approach?

So, watch this space to see how the idea develops. I’m also interested in your opinions and experiences with starting and cooperating with non-profits if you have any.

Zemanta Pixie

Posted by on August 11, 2008 in Career, Community, Research


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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 – 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.

Zemanta Pixie

Posted by on July 28, 2008 in Comments, Community


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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?


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


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Computational Biology and Evolution – new blog

[via Simon Greenhill at Henry] Alexei Drummond, scientist at Department of Computer Science at University of Auckland and Chief Scientist at Biomatters Ltd, has launched a blog: Computational Biology and Evolution.

We grow stronger…

1 Comment

Posted by on November 21, 2007 in bioinformatics, Community


Bio::Blogs #16 – Halloween edition

Blogs #16

Original image courtesy of Flickr user docman

Welcome to the 16th edition of Bio::Blogs, the monthly digest of highlights from bioinformatics and computational biology blogs. Hat tip to Deepak for suggesting the name (we actually start to absorb many sides of Halloween here in Poland).

Everyday science

This time we have interesting post on day-to-day scientific life in three categories: issues of scientific communication, bioinformatics workspace and software tips and news.

Michael Barton from Bioinformatics Zen posted three stories explaining how web technologies may improve scientific communication, plus he shared his thoughts about developing skills that are rarely taught in a grad school. “As for your research, start a blog”, he writes, “(…) Try alternative communication formats, post videos on your research, persuade other members in your lab as well.” As we speak about alternative formats, you’ve probably heard about Second Life and SciFoo virtual talks. If SL still feels awkward to you, Sandra Porter from Discovering Biology in a Digital World wrote a gentle introduction to attending a Second Life poster session.

From Neil Saunders we have an excellent tutorial (part I and part II) about setting up and using SVN and Trac for tracking bioinformatics projects. In theory, scientists should be able to trace anything they release (not only source code) back to its origins and Neil has ready to implement solution. As Paulo Nuin from Blind.Scientist found Trac a little bit clumsy, he recommended svn-time-lapse instead, since it’s easier to compare two versions of the file (see part I and part II). You can test both approaches with your new project inspired by Tiago from Perfect Storm – he started an interesting journey with Scala for bioinformatics.

There are around 10 new software releases every hour at Fortunately pool of scientific software is more manageable. This month’s highlights are: good news from Noel O’BoyleFrog developers donated their code to OpenBabel (that means flexible command-line converter from 1D/2D descriptors of molecules to 3D structure in a near future), tip from Andrew Perry about starting Qutemol, simple but impressive molecular visualizer, under linux (hint: use Windows version), reports from Animesh Sharma on the new versions of Biopython and Bioconductor.

Outside these categories there is a post of Jason Isheng Tsai from Paradoxus (good timing, only hour and a half before finishing this post) about his usual day in front of a computer. If you do have friends who are not scientists (do you? 🙂 ) asking about your work, you can point them there, although I have a feeling that they may not understand the irony in a difference between “grant version” and “real version” of the scientific work…

Trends, predictions and analysis

October started with announcement from IBM Research about software for 3D visualization of patient’s medical records. Bertalan Meskó from ScienceRoll posted his interview with Andre Elisseeff, who leads the healthcare projects at IBM Zurich Research Lab. Elisseeff says they got very positive feedback from physicians that used this “Google Earth for human body”. Maybe this and other health-related news were inspiration for Pedro Beltrao to write a brilliant story about possible future of personalized genomics. Frightening stuff.

Managing data across therapeutic programs can be challenging, not only because of their amount, but also because of difficulties in sharing information stored in there. Deepak Singh posted his thoughts on a topic of persistent context, this is maintaining context of the information along with the information. For me the eye-opening sentence was: “If you are storing relationships, i.e. your queries, and treating them as pieces of data, you are essentially capturing relationships, and the semantic web provides an elegant framework to do so.”

Open access

I am happy to point you to a post of Michael Kuhn about Max-Planck Society canceling its subscription to Springer journals. Reason for canceling? Way too expensive subscription (if paying individually for each downloaded paper is considered cheaper, such subscription is too expensive). Can you see a smile on faces of publishers of open-access journals?

If this issue resonate with you, have a look at the Evolgen highlight – an editorial in PLoS Biology entitled “When Is Open Access Not Open Access?” (–important update– see Pedro’s comment to that editorial), and point your colleagues who are not yet aware of significant changes we are facing to screencast of

Research highlights

One of the things I found interesting this month were two posts of Ian York from Mystery Rays from Outer Space. He wrote about publication demonstrating a potent epitope from HIV that emerged from a frame-shifting event and raised a question if this is a major phenomenon. As far as I know, out-of-frame sequences were not yet thoroughly analyzed – is it a chance for smart bioinformatics?


Scientific blogosphere is getting older: this month Omics! Omic! written by Keith Robinson turned one.

So, that’s all for this month. I apologize if anybody felt omitted but you have a good chance to pay me back by claiming the next edition of Bio::Blogs (just send an email to bioblogs at gmail dot com). I also want to thank Pedro Beltrao for giving me a chance to host this edition, despite my apparent bastardization of English language.


Posted by on November 1, 2007 in bioblogs, bioinformatics, Community


Bio::Blogs #16 – call for submissions

I got the privilege of hosting the next edition of Bio::Blogs. If you have anything you would like to have included please send an email to szczesny dot pawel at gmail dot com or to bioblogs at gmail dot com before 1st of November.


Posted by on October 20, 2007 in bioinformatics, Community


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