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Joining ONS club – classification and prediction of bacteriocins

03 May

It’s finally the time to jump in into Open Notebook Science pool with my small project: classification and prediction of bacteriocins. Main page of this project is on Freelancing Science wiki: freelancingscience.wikispaces.com/bacteriocins. After reading recent post by Michael Barton on ONS , I’ve decided to stick only to wiki – I had already another blog set up for this project, but if blog doesn’t work very well for Michael, I doubt it will work for me. Since it’s completely side project, updates on the project blog on would be embarassingly rare. So far the wiki doesn’t contain much of a data, nothing more than a plan in fact. But I think it’s important to at least start somewhere.
Direct inspiration for the project was this post at Microbiology Blog. It describes results of some experiments on growth inhibition of bacteria by haloarcheal organisms, which could be in some cases explained by novel archeocins, peptide or protein antibiotics from Archea. After quick look I realised, that I see sequence similarity between seemingly non-related bacteriocins. That of course lead to a question if I am able to repeat the procedure from my PhD project – understand the protein family, and then write an annotation/prediction tool. I don’t expect outstanding results but at least this will be a good occasion to document my approach to protein sequence annotation. So if not scientific, it should have at least a little of educational value.

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4 Comments

Posted by on May 3, 2008 in bioinformatics, Research

 

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4 responses to “Joining ONS club – classification and prediction of bacteriocins

  1. Mike

    May 4, 2008 at 10:52

    So far the wiki doesn’t contain much of a data, nothing more than a plan in fact. But I think it’s important to at least start somewhere.

    I strongly agree with this statement. In my opinion ONS is, at the moment, about just starting anything then building on it. Focus on what works and drop what doesn’t.

     
  2. Cameron Neylon

    May 4, 2008 at 13:42

    Great news! Definitely agree that it is more helpful to get started than to worry about it being perfect from the beginning. I think there is still a place for a blog in the mix because it helps to reconstruct the history of ideas when you need to go back to things. Having some form of index which is timeline of ‘current mental state’ is important I think but it possibly doesn’t need a separate blog all of its own as long as you can get at the material.

     
  3. Deepak

    May 4, 2008 at 14:09

    I can’t agree more with the comments above. I don’t think you need a separate blog either. Have the Wiki be the “repository” and the existing blog the “commentary” and I think you’re in good shape.

     
  4. Jean-Claude Bradley

    May 4, 2008 at 17:31

    Awesome! Yes it is sufficient to update milestones on this blog and use the wiki for details. People can subscribe to your wiki by clicking on recent changes then notify on Wikispaces. That can be in the form of email or RSS feed. If the number of changes is few this is a good strategy. But if there is lots of activity it gets annoying and really hard to follow – thus the advantage of the blog updates.

     
 
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