Welcome to Bioinformatics/Biocomputing Information Repository

Overview

In this site, you will find

• Information about computing resources/application packages available on LONI (www.loni.org) High Performance Computing (HPC) systems
  

• Useful links for bioinformatics/biocomputing tools
• Science gateway providing LONI resources (HPC systems and scientific applications for biocomputing).  MrBayes, a Bayesian Inference of Phylogeny program, and NAMD, a scalable molecular dynamics simulation packages are planned to be available in the near future.  (To use this service, you must register. For any questions, contact us.)

NEWS:

Presentation materials from the 2nd LBRN Computational Biology Workshop are available from here. 

Getting Started

For information about

• How to get an account and an allocation on LONI machines :  Find information here
  
• How to get LONI grid certificate :  Find information here
  

LONI HPC Systems and Available Software

LONI Systems INFO : http://www.loni.org/systems/help/
LONI Documentation : https://docs.loni.org/wiki/Main_Page

Useful Links for Bioinformatics/Biocomputing

NAMD on LONI Linux Cluster

Sequence Alignment and Phylogeny tools

mplBLAST  :    http://www.mpiblast.org
clustal-mpi :  http://www.bii.a-s    
 tar.edu.sg/achievements/applications/clustalw/download.php

Tcoffee and more : 
        http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi    

PHYLIP : http://evolution.genetics.washington.edu/phylip.html 
PAML : http://abacus.gene.ucl.ac.uk/software/paml.html
PAUP : http://paup.csit.fsu.edu/
MrBayes :  http://mrbayes.csit.fsu.edu
BAli-Phy : http://www.biomath.ucla.edu/msuchard/bali-phy/

ARB project :  http://www.arb-home.de/
Silva project : http://www.arb-silva.de/

RNA Sequence and Structure Analysis

Nucleic Acid Database (NDB) :
http://ndbserver.rutgers.edu/index.html
Prediction Software : 
http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software
RNA related software : (The RNA World Web Site)
http://www.fli-leibniz.de/RNA.html#Software

Molecular Dynamics

AMBER : http:///amber.scripps.edu/
NAMD : http://www.ks.uiuc.edu/Research/namd/
GROMACS : http://www.gromacs.org
LAMMPS : http://lammps.sandia.gov/
TINKER : http://dasher.wustl.edu/tinker/

Docking

AutoDock : http://autodock.scripps.edu/
AutoDock Vina : http://vina.scripps.edu/
UCSF DOCK : http://dock.compbio.ucsf.edu/

Bioinformatics Portals

Mobyle Project : http://bioweb2.pasteur.fr/projects/mobyle/
Renaissance Computing Institute (RENCI) Bioportal : 
http://www.renci.org/resources/software/bioportal.php
SWAMI, Next Generation Biology Workbench : http://www.ngbw.org/
Life Science Gateway (A teragrid science gateway) : http://lsgw.mcs.anl.gov/
Teragrid Science Gateways : http://www.teragrid.org/programs/sci_gateways
SimBios (NIH Center for Biomedical Computation at Stanford U.) :
http://simbios.stanford.edu

 Data Mining Tools

Weka : http://www.cs.waikato.ac.nz/ml/weka/
R : http://www.r-project.org/

Structure Visualization Tools

VMD : http://www.ks.uiuc.edu/Research/vmd/
PyMOL :  http://www.pymol.org
UCSF Chimera : http://www.cgl.ucsf.edu/chimera/
COOT : http://www.ysbl.york.ac.uk/~emsley/coot/

   Miscellanies

Sequence utils (conversion) :
   http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html

Additional Useful Links

PDB database : http://www.rcsb.org/pdb/home/home.do

Other HPC systems with CCT

(Note) To use these LSU owned systems, please contact us.

Our Science Gateway Development for LBRN community