Open Source Software distributed by the Research and Academic Computing Division of UITS
fastDNAml - fastDNAml is a program that infers evolutionary histories from genetic sequences. fastDNAml was developed with the support of a Shared University Research Grant from IBM, Inc. and by the Indiana Genomics Initiative.
CATPA - This portal provides a library of family curations together with an available application - the Curation and Alignment Tool for Protein Analysis (CATPA) - that allows for the management and visualization of curation and annotation data at the residue level including deletions and motifs. The initial development of CATPA was supported by the IBM Life Sciences Institute of Innovation grant to IU, a joint development contract with IBM, Inc. to M. Dalkilic and C.A. Stewart, as well as funding provided by University Information Technology Services.
Pubs Online - Pubsonline is an open source tool for the management and presentation of databases of citations via the web. Pubsonline was developed by the Unix Systems Support Group within UITS.
Batch Scripts - These batch scripts were designed to simplify use of the IBM SP. They were developed by the Bioinformatics support group within UITS.
SMBL - Simple Message Brokering Library (SMBL) is a framework for MPI programs using ephemeral resources. It was designed for parallelizing scientific programs to be run on sporadically-available systems (such as Windows desktop systems), and has been implemented in conjunction with Condor.
NBPack - a set of functions and datat structures that implement hierarchical tree methods for classical N-body simulations. NBPack was developed with the support of a Shared University Research Grant from IBM, Inc.
PViN - PViN (Pedigree Visualization and Navigation) is a scalable visualization and analysis tool for very large pedigree databases. PViN was developed by the UITS Advanced Visualization Lab with support from the Indiana Genomics Initiative. (presently in beta testing; licensing TBD)
XLiveCD - XLiveCD allows users of Microsoft Windows to connect to remote Unix computers, run graphical applications and have the graphics displayed on their desktops. The software runs from the CD without being installed. XLiveCD was prepared by University Technology Services to facilitate use of research Unix systems at Indiana University by Windows users on campus.
CLSD Parsers and Update Scripts - The Centralized Life Sciences Data (CLSD) service provides a single, SQL-based interface for querying a variety of public Life Sciences Data, including BLASTable sequence databanks and non-relational datasets that have been transformed into relational tables. CLSD is implemented using IBM's data federation technology, Information Integrator, which includes IBM's DB2 Relational Database. IU open source contributions include data ingets parsers and data updating scripts for use IBM DiscoveryLink/DB2. CLSD was eveloped with the support of a Shared University Research Grant from IBM, Inc. and by the Indiana Genomics Initiative.
GeneIndex - a program for indexing words within a genome. GeneIndex was developed with the support of a Shared University Research Grant from IBM, Inc. and by the Indiana Genomics Initiative.
PENELOPE-MPI - MPI parallel version of a radiation transport code. PENELOPE-MPI was developed with the support of a Shared University Research Grant from IBM, Inc. and by the Indiana Genomics Initiative. (Community code; controlled as a mutation.)
Tree3D - a tool for comparing and visualizing trees resulting from phylogenetic computations. Tree3D was developed with support from the Indiana Genomics Initiative.
PINY_MD for AIX - PINY_MD(c) is a multipurpose, object-oriented molecular simulation package developed as a collaborative effort between Indiana University, New York University and the University of Pennsylvania. An AIX implementation of the PINY_MD software was created by UITS with the support of a Shared University Research Grant from IBM, Inc. and by the Indiana Genomics Initiative.
3DIVE - 3DIVE (3D Interactive Volume Explorer) is an immersive visualization tool for volumetric data. Development of 3DIVE was supported in part by NSF Grant CDA-9601632. (Software available as binaries only.)
XMView - XMView is a scalable visualization tool for crystallographic molecules. It is available in desktop and immersive (CAVE) versions. Development of XMView was supported in part by NSF Grant CDA-9601632. (Software available as binaries only.)
