10/26/11

Nonsense article

Several months ago I have asked the question in the BlueObelisk QA site about what to do with nonsense article?


I need you advice: I have saw an accepted article in the journal about molecular modeling – QSAR, homology modeling, no wet-lab experiments. And I definitely can say that the article is total nonsense – the binding site is absolutely incorrect and QSAR data and interpretation treated terribly!

So, the question: what to do? write a letter to the editor?

And general question to discussion – What to do if you think that the article is incorrect not in terms of science hypothesis, but in terms of general sense? Authors have used incorrect data, or interpret results absolutely incorrectly.

Update: Wrote a letter to editor-in-chief of the journal. Will keep you with updates.


But the editor doesn't answer my anything. So, time to open the article name and explain why I think it is nonsense, but first of all I do not have any personal dislike of the authors or whatever, I am talking about science.

So, here is the article in Chemical Biology & Drug Design: A Structure-based QSAR and Docking Study on Imidazo[1,5-a][1,2,4]-triazolo[1,5-d][1,4,]benzodiazepines as Selective GABAAα5 Inverse Agonists.

Here are my points:

1. GABAA receptor is heteromeric receptor. Authors don't care about this, and have treated it as homopentameric.

2. It's well known that benzodiazepine binding site is formed by alpha and gamma subunits, and definitely binds in extracellular region and definitely not in the transmembrane domain (a lot of point mutation studies confirmed this). Authors didn't discuss any reasons for selecting the binding site at all.



3. QSAR...the correlation coefficient of predicted versus real I think will tell a lot. Q2 of 0.7 is really good...but if authors will remove all data above 20 affinity log values I think they will receive even 0.9.



Comment: I quit don't agree we Noel O'Boyle: "Just concentrate on doing your own work well. Our job as scientists is not to police the chemical literature. Weak, or wrong, papers are their own reward." Yes, we should concentrate on the science as our main job, but we are the part of the community and somehow we are responsible for the noise that society produce.

10/17/11

Using python3.0 under standard ubuntu python2.6.6 installation

I have default python2.6.6 installation on my machine, but I want to use the new version of the python3.0 for some scripts. The script.py is simply printing the Python version used, but with shebang version specified.

#!/usr/bin/python3.1
import platform
print(platform.python_version())



So, the results are following.
1. Starting the script from command line python test.py will give us the default version

2. Starting the script from command line with specified the version python3.1 test.py will give us the 3.1 python version.

3. If we remove the shebang line, so the script will behave absolutely the same, but ./test.py will fail, when launching with shebang line ./test.py - it will give us the correct 3.1 version. Launching without shebang line this way python3.1 test.py also will give us the 3.0 version.

10/12/11

PhD position in folktale classification and clustering

Reading the RSS of EURAXESS site, I found a very interesting position: PhD position in folktale classification and clustering. Sounds very funny from first point of view, but in reality is really excitement to use text mining and Natural Language Processing to analyze the myths and folktales.

Description
Master degree in computer science, natural language processing, artificial intelligence or a related discipline (with a specialization in natural language processing)
Knowledge of, and preferably practical experience with, corpus-based methods for text analysis, machine learning, document classification and/or clustering
Good programming skills





Make a PCA of the dragon!
Train neural network based on Cinderella!
Make the ant colony based on gnomes!