BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//CERN//INDICO//EN
BEGIN:VEVENT
SUMMARY:DNA muligene approach on HPC using RAxML software
DTSTART;VALUE=DATE-TIME:20121017T103000Z
DTEND;VALUE=DATE-TIME:20121017T110000Z
DTSTAMP;VALUE=DATE-TIME:20261011T060242Z
UID:indico-contribution-95-162@indico.ipb.ac.rs
DESCRIPTION:Speakers: Luka Filipovic (University of Montenegro)\nComputati
 onal phylogeny is a challenging even for the most powerful supercomputers.
  One of significant application in this area is Randomized Axelerated Maxi
 mum Likelihood (RAxML) which is used for sequential and parallel Maximum L
 ikelihood based inference of large phylogenetic trees. \n\nWe choose 5 dif
 ferent genes\, two real genes (part of  D-loop and Cytochrome b of differe
 nt European salmond fish species) both from mitochondrial genome and addit
 ional three designed genes in order to test reliability of constructed cen
 sus phylogeny tree. Two of those “fake” genes were designed with phylo
 geny information similar to phylogeny of real genes while the third one wa
 s completely different. Using of multigene option of RAxML software we tes
 t contribution of each gene (percentage of base pares in tested genes) in 
 terms of gene contribution in phylogeny tree construction. We additionally
  test contribution of gene position in analysis in terms of final results 
 of phylogeny reconstruction. \n\nThis paper will also cover scalability re
 sults of multigene tests on high-performance computers for coarse and fine
  grained parallelization using MPI\, Pthreads and hybrid version.\n\nhttps
 ://events.saifa.rs/event/291/contributions/162/
LOCATION:National Library of Serbia
URL:https://events.saifa.rs/event/291/contributions/162/
END:VEVENT
BEGIN:VEVENT
SUMMARY:A new microRNA target prediction tool identifies a novel interacti
 on of a putative miRNA with CCND2
DTSTART;VALUE=DATE-TIME:20121017T093000Z
DTEND;VALUE=DATE-TIME:20121017T100000Z
DTSTAMP;VALUE=DATE-TIME:20261011T060242Z
UID:indico-contribution-95-165@indico.ipb.ac.rs
DESCRIPTION:Speakers: Anastasis Oulas (IMBG-HCMR)\nComputational methods f
 or miRNA target prediction vary in the algorithm used\; and while one can 
 state opinions about the strengths or weaknesses of each particular algori
 thm\, the fact of the matter is that they fall substantially short of capt
 uring the full detail of physical\, temporal\, and spatial requirements of
  miRNA::target-mRNA interactions.  Here\, we introduce a novel miRNA targe
 t prediction tool called Targetprofiler that utilizes a probabilistic lear
 ning algorithm in the form of a hidden Markov model trained on experimenta
 lly verified miRNA targets. Using a large scale protein down-regulation da
 taset we validate our method and compare its performance to existing tools
 . We find that Targetprofiler exhibits greater correlation between computa
 tional predictions and protein down-regulation and predicts experimentally
  verified miRNA targets more accurately than 3 other tools. Concurrently\,
  we use primer extension to identify the mature sequence of a novel miRNA 
 gene recently identified within a cancer associated genomic region and use
  Targetprofiler to predict its potential targets. Experimental verificatio
 n of the ability of this small RNA molecule to regulate the expression of 
 CCND2\, a gene with documented oncogenic activity\, confirms its functiona
 l role as a miRNA. These findings highlight the competitive advantage of o
 ur tool and its efficacy in extracting bio-logically significant results.\
 n\nhttps://events.saifa.rs/event/291/contributions/165/
LOCATION:National Library of Serbia
URL:https://events.saifa.rs/event/291/contributions/165/
END:VEVENT
BEGIN:VEVENT
SUMMARY:Quantum-Chemical Calculations for the Quantitative Estimations of 
 the Processes in DNA
DTSTART;VALUE=DATE-TIME:20121017T100000Z
DTEND;VALUE=DATE-TIME:20121017T103000Z
DTSTAMP;VALUE=DATE-TIME:20261011T060242Z
UID:indico-contribution-95-185@indico.ipb.ac.rs
DESCRIPTION:Speakers: George Mikuchadze (Programmer in Georgian Research a
 nd Educational Networking Association - GRENA)\nInvestigated the DNA tende
 ncy to denaturation using Dencity Functional(DFT) Theory method.\nPresence
  of the polaric solvents with small polarity index Et - such as ethanol\, 
 in the aquatic ambient causes protons transfer between nucleobases pair\, 
 which in turn fires DNA denaturation and mutation proceses. Using Software
  for analysing chemical compounds the tautomeric equilibrium indexes of th
 e nucleobases were calculated. The software was ported on the HPC (NCIT-Cl
 uster) infrastructure.\n\nhttps://events.saifa.rs/event/291/contributions/
 185/
LOCATION:National Library of Serbia
URL:https://events.saifa.rs/event/291/contributions/185/
END:VEVENT
END:VCALENDAR