4/25/12

BioIT Eorld 2012 - day two

I think BioIT World is the biggest conference in the world that mix life science and informatics. All of the molecular modeling software developer monsters were presented here: ChemAxon, OpenEye, Accelrys. GGA software was a specific interest for me, first because molecular modeling software development team is located in Saint Petersburg, one of the most beautiful Russian cities, second - because of their open source initiative - Bingo, Indigo and Imago. Also, a lot of companies representing data mining, data management and integration spheres were there. 

Some hardware companies were also active: I have tested the real-time rendering of the proteins - it's really hot, especially when you have two Tesla GPU cards. Personal super computers are reality nowadays - money is the only question.
 
Special news is cloudification of the Pipeline Pilot. Hmm...let it be the new word - cloudification, because people want to put into the cloud everything they have.

Actually, the conference have one big minus - there are 12 really interesting parallel tracks all at once! 


  • IT Infrastructure – Hardware
  • IT Infrastructure – Software
  • Cloud Computing
  • Bioinformatics
  • Next-Generation Sequencing Informatics
  • Systems and Multiscale Biology
  • eClinical Solutions
  • eHealth & HIT Solutions for Personalized Medicine
  • Drug Discovery Informatics
  • Molecular Diagnostics Informatics
  • Open Source Solutions
  • Cancer Informatics
So, after thorou inspection I chose Systems and Multiscale Biology, Drug Discovery Informatics and Cloud Computing, as my area of expertise. Here is the summary.


Introducing eTRIKS: European Translational Information & Knowledge Management Services - management and integration of the medical and life science data for translational medicine on the basis of open-source solution tranSMART.


Library Enhancement through the Wisdom of Crowds - Agrafiotis is really a big figure in computer-aided drug design that work for JnJ. Agrafiotis team randomly selected compounds from in-house database, then added some real HTS compounds from the library with good known physico-chemical profile. After, this database was given to 1000 medicinal chemist to select good compounds for HTS manually using "good-neutral-bad" scheme. Finally, it was shown that the most of the manually selected compounds have good solubility, good lipophilicity and good synthetic accessibility. That was really impressive, human brain definitely have best learning algorithm. The only thing that is disturbing is that the possibility of the "good" selected compound to be be rejected is around 20%. So, crowd-sourcing drug design is the future?


Changing the Landscape of Laboratory Informatics Systems to Enhance Innovation Life Cycle Management (ILM) - some impressive Accelrys and Scitegic lecture about scientific data management. Too expensive guys!


Chemical-Protein Interactome and its Application in Personalized Medicine and Drug Repositioning - using docking with Dock (not the best docking tool) FDA drugs were docked to all possible targets from PDB. Olanzapine and clozapine were used as an example: the last one cause agranulocytosis in 1% of the patients. What authors found that the HSP70 is over-expressed in microarray from the cancer line (strange, all of the HSPs are over-expressed in cancer lines), and also this target was found in the top of the inverse screening target list. Patients with agranulocytosis have mutation in one amino acid in the binding site that actually gave improved DOCK score for clozapinebut not olanzapine, that is actually is cause of the side effect. So, for me these results are very interesting as success for chemogenomics but still very-very questionable. DOCK have only ~60% success in Virtual screening.
Next Generation Bioinformatical Analysis on the Cloud - very interesting, but do we really need to put genome assembling into the cloud?


OpenEye Grapheme - very nice 2D depiction of the ligand-receptor complexes (soon will be avaliable in Vida) and new coloring and depiction scheme for compounds.


Also, it was interesting to talk with author of JSDraw and test new product - TouchMol a chemical editor for tablets, very nice and easy to draw compounds with fingertips, but I also think desktop users will like it. Have small talk with one of the Aysdi employers - interesting topological mapping as visualization for for biological networks.