The Core Facility is charged with providing support for the computational biology and bioinformatics software most used at both institutions. We have already established a substantial software library and are providing support for a number of laboratories. We have already provided assistance to several existing laboratories in setting up software and solving software- and hardware-related problems.
The Core Facility also coordinates and manages software site licenses to dramatically decrease the expense of outfitting individual machines with individual software licenses. We have set up floating licenses for a number of software packages now widely used within the two campuses including MATLAB, GeneSpring, and Igor. This has resulted in substantial cost savings to both institutions as well as made the software available to investigators who could not otherwise afford it. In addition to providing software, the facility will also manage training sessions and workshops on its use. Two such workshops are scheduled. Representatives from Genespring and Affiametrix will hold workshops in April 2006.
Currently the following software is available for use on our systems:
To view a software description hold your mouse cursor over the name of the software. Javascript must be enabled. Some software names have links available for their homepage and tutorials.
| AutoAligner | Imaris |
| Fasta-protein | Fasta-nucleotide |
| GenScan |
| Fasta-ASD server | Fasta-LGIC Protein server |
| Fasta-LGIC Nucleotide server | Fasta-Proteome server |
| Fasta-Genome server | Fasta-SNP server |
| Fasta-WGS server | GENESIS (General NEural Simulation System) tutorial |
| GeneSpring tutorial | HMMER tutorial |
| Igor Pro tutorial | InterPro tutorial |
| MATLAB tutorial | MATHEMATICA tutorial |
| McClade | MEGA (Molecular Evolutionary Genetics Analysis) tutorial |
| MFOLD (RNA & DNA Folding Applications) | MySQL (Open Source Database) tutorial |
| Neuron tutorial | PAUP (Phylogenetic Analysis Using Parsimony) tutorial |
| PDQuest | Phylip |
| PredictProtein tutorial | RasMol (Molecular Graphics Visualization Tool) tutorial tutorial |
| SAM (Significance Analysis of Microarrays) tutorial tutorial | SeaView tutorial |
| TreeView tutorial | VMD tutorial |
Phred/Phrap/Consed/PolyPhred more info
| Phred | Phrap | Consed | PolyPhred |
| Meme | Mast |
Lagan Alignment Toolkit: comprised of these four modules.
| Chaos | Lagan | |
| Multi-Lagan | Shuffle-Lagan |