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Monthly Archives: October 2008

Qutemol and Ubuntu – native support

A Snapshot of the QuteMol open source software...

Image via Wikipedia

A week ago I got an email from a long-time-no-see friend, Marcin Feder, with information that Qutemol works fine on the Hardy and Gutsy versions of Ubuntu (binary packages were prepared by Morten Kjeldgaard; see more https://blueprints.launchpad.net/~mok0/+related-software, there are some other interesting titles there). According to Marcin following steps are enough to enjoy Qutemol on your linux box:

sudo aptitude install libungif4g  libwxbase2.8-0 libwxgtk2.8-0
wget http://mirrors.kernel.org/ubuntu/pool/main/g/glew/libglew1.4_1.4.0-1ubuntu1_i386.debhttp://ppa.launchpad.net/mok0/ubuntu/pool/main/q/qutemol/qutemol_0.4.1~cvs20080130-0ubuntu1~gutsy~ppa1_i386.deb
sudo dpkg -i libglew1.4_1.4.0-1ubuntu1_i386.deb
sudo dpkg -i qutemol_0.4.1~cvs20080130-0ubuntu1~gutsy~ppa1_i386.deb
I have too ancient Ubuntu version to check it right now, but not all of you are so lazy with upgrades so have fun.
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Posted by on October 16, 2008 in Visualization

 

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Personal Development for Smart People: review of Steve Pavlina book

Personal development wasn’t so far the subject of any post on this blog, and that’s not a surprise – it’s hard to hard to measure, hard to study and full of published trash. However, I’m interested in the topic and one of my favourite blog on the topic is “Personal Development for Smart People” written by Steve Pavlina. While Steve is quite controversial (as you’d expect from somebody who develops his physic abilities, is a raw foodists and experiments with polyphasic sleep) and I sometimes strongly disagree with him or have a hard time believing in some stories, often enough he writes very interesting and useful articles.

When he announced that his book will be released in October, I was planning to buy it but I got a pre-release as a part of promotion offer. The offer required to post a review, not to praise the book, so here’s my honest and biased opinion.

I will not go into detail on the contents of the book. You can get a pretty good feeling what it is about here. The book doesn’t overlap very much with excesive content of Steve’s blog – most of the practical issues of self-development are covered on the blog, the rest is pretty much original.

This is not an easy book and it will not leave you happy and motivated. It’s not easy not only because it requires some basic knowledge (for example, Law of Attraction mentioned few times is not defined anywhere), but it will ask you to question lots of your beliefs and assumption. For example, Steve asks to rate several aspects of your life, and then re-rate anything below 8 as 1, claiming that if you don’t have exactly what you really want, you simply don’t have it, period. You can call it a trick, but taking it seriously may be somehow difficult. Also, it doesn’t have any motivational stories, it doesn’t call you to act or to punch your chest – it has just down to earth description of the process of personal growth. My biggest complain was that it was too short – it felt like an introduction, not comprehensive guide. Also, from a scientist point of view (I know, this is not research paper) I missed some background and comparison to ideas other people have written over the years.

You can read this book and extract lots of practical hints on how to achieve something faster/more efficiently, or how to develop necessary habits, but it’s not definitely why this book was written – from my perspective it’s an invitation to think more seriously about personal growth and to challenge the status quo of what we think about ourselves. And I would like to accent the word “invitation”. Steve is not aggressive and does not try obsessively to prove he is right (as it happens too often in other books). It’s an invitation you don’t have to answer.

What’s in this book for scientists? That’s a hard question. This book wasn’t written for scientists, poker players, truck drivers or startup founders. It was written for people who want to grow and need some help on the way. Definitely, it can serve as a reminder that even science should be ethical and should provide a value, but on the other hand I don’t think majority of you need that reminder at all. As a side note, Steve explains in the book why scientists (and other professions) are paid so little (he calls it low social value), but we knew that anyway :) .

What I got from the book was help in making my non-profit plans more clear. Although you don’t need to start a non-profit to find this book worth reading.

You can order the book at Amazon.

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Posted by on October 16, 2008 in Comments

 

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Open Access Day

Today is the world’s first Open Access Day . It aims at broadening awareness and understanding of OA. The approach is to make as many people as possible to blog today on the topic, possibly answering the following questions:

  • Why does Open Access matter to you?

In my case, where pretty soon I’ll have no support from a large institution, Open Access means ability to do research. OA is a vital help to small or underfunded research groups.

  • How did you first become aware of it?

Internal policy of my former employer required that all results should be published in OA journals. BTW, it didn’t change since then.

  • Why should scientific and medical research be an open-access resource for the world?

Ability to do research and to innovate shouldn’t be inhibited by access to knowledge and data produced by publicly funded research institutions.

  • What do you do to support Open Access, and what can others do?

I do publish in OA journals (four out of five publications I have so far are OA).

See more OA Day entries at FriendFeed Open Access Day room.

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Posted by on October 14, 2008 in Community, Research

 

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Many Eyes and literature summary

I’m not the first one to come up with this idea – Ntino posted about it before. However, I didn’t really understand before how powerful it could be. Using Many Eyes visualization capabilities I’ve created a quick browsable summary of abstracts related to a particular protein. I took all abstracts PubMed returned for a particular query (in this case it was “YadA Yersinia”; YadA is a prominent adhesin and important pathogenicity factor in Yersiniae) and uploaded them as text into Many Eyes. I chose “Word Tree” representation and searched for “yada”, which gave a nice graph of the most prominent phases related to this protein/gene name. Maybe it’s not a breakthrough, but compared to the classification/semantification provided by GoPubMed, such approach works much better for entities that aren’t well described in biological ontologies.

Given that the whole concept is pretty straightforward, it would be nice if one of alternative PubMed search engines provided a similar method of summarizing user’s query, don’t you think?

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Posted by on October 4, 2008 in Papers, Research, Visualization

 

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