Software
Phoretix 2D Evolution
Phoretix 2D Evolution provides a comprehensive solution for 2D gel analyses of all kinds, from simple single-gel analysis to more complex multiplexed gel experiments. From spot detection and quantitation to differential expression analysis, Phoretix 2D Evolution gives a convenient workflow for 2D gel experiments, regardless of the staining methodology used.
ArrayAssist
Analysis of microarray data is far more daunting than running the array itself. The CIB has acquired ArrayAssist to help researchers using our Affymetirx Core lab translate their data into biologically meaningful results. ArrayAssist provides basic statistical analysis techniques for experiments of simple design all in a graphical environment.
PathwayAssist
PathwayAssist provides a sharp graphics production tool with advanced data mining techniques to take potentially abstract statistical data and translate it into visually and biologically meaningful results. PathwayAssist will construct a publication quality diagram of significant pathways with all nodes and connections, as well as find annotation and publication data related to each pathway component.
Pathway Tools
The Pathway Tools suite of software applications helps researchers to create, curate, and utilize pathway databases. Powerful inference algorithms are used to assemble signaling and metabolic pathways. Genomic or proteomic data may then be "painted" on top of the database pathways to elucidate relationships and patterns related to a given experiment.
iNquiry
iNquiry Bioinformatics Portal »
With the Apple Workgroup Cluster, the CIB stands ready to offer computing resources for demanding bioinformatics applications. The cluster hosts 170+ well-known applications(.doc), including many protein and DNA sequence analysis tools. Additional applications may also be incorporated as needed to accommodate the future needs of USU researchers.
SAM for Excel
Deployed as a plugin for MS Excel, SAM (Statistical Analysis of Microarrays) gives the user control over the false discovery rate and returns significant genes at the given level. The user pastes the data into a worksheet and a few clicks later a list of significantly induced and repressed genes is given as output.
DNAStar
DNAStar has the following capabilities:
- EditSeq-- Edit and import sequences and annotations
- MapDraw-- Restriction Site Analsis and Map Creation
- MegAlign-- Multiple and Pairwise Sequence Alignment
- PrimerSelect-- Comprehensive Oliognucleotide Design
- Protean-- Protein Structure Discovery, Annotation and Publication
- SeqMan-- Sequence Assembly and Contig Managemen
- GeneMan-- Biological database access