Note: Software Database is still being populated.
Software / Bioinformatics | |
| Bioconductor Version(s): 1 | Support: None Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. | |
| biojava Version(s): 1 | Support: Onsite BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit. Machine(s):
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| bioperl Version(s): 1 | Support: Onsite The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. Machine(s):
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| blacs (Basic Linear Algebra Communication Subprograms) Version(s): 1 | Support: None The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. | |
| blas Version(s): 1 | Support: None Basic Linear Algebra Subprograms | |
| Chemical Database Version(s): 1 | Support: Onsite Developed and implemented alpha test versions of chemical databases supporting high throughput screening and combinatorial chemistry. In the former case, bioactivity screening data is stored in a table indexed according to a large number of chemical compounds available at the University of Kansas High Throughput Screening Center. In the latter case, structures are stored by chemists developing and analyzing chemical libraries. In both cases the databases are searchable by chemical structure, compound ID and physicochemical properties. Functional demonstration accounts have been created for this report and can be accessed at the following URLs: http://kumgms01.msg.ku.edu:8080/hts/ http://kumgms01.msg.ku.edu:8080/combichem/ | |
| clustalw Version(s): 1 | Support: Onsite Performs multiple sequence alignments Machine(s):
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| dms Version(s): 1 | Support: None Dms calculates the molecular surface of a molecule. The molecular surface resembles the van der Waals surface of a molecule, except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated. The surface includes cavities in the interior of the molecule, even if they are not accessible to a solvent molecule coming from the outside. | |
| dock6 Version(s): 1 | Support: Corporate DOCK 6 is written in C++ and is functionally separated into independent components, allowing a high degree of program flexibility. Accessory programs are written in Fortran 77. We provide source code for all programs. | |
| emboss Version(s): 2 | Support: Onsite EMBOSS, The European Molecular Biology Open Source Software Suite, is a package of high-quality FREE Open Source software for sequence analysis. Machine(s):
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| genscan Version(s): 1 | Support: Onsite GENSCAN is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants. For each sequence, the program determines the most likely "parse" (gene structure) under a probabilistic model of the gene structural and compositional properties of the genomic DNA for the given organism. Machine(s):
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| hmmer Version(s): 1 | Support: Onsite HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. Basically, you give HMMER a multiple sequence alignment as input; it builds a statistical model called a "hidden Markov model" which you can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family. Machine(s):
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| NCBI Tool Kit Version(s): 1 | Support: Onsite Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. Machine(s):
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| PBlast Version(s): 2 | Support: Onsite PBlast application developed by Terry Clark. | |
| PISE Version(s): 1 | Support: Onsite a tool to generate Web interfaces for Molecular Biology programs Machine(s):
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| R Version(s): 1 | Support: Onsite R is a free software environment for for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Machine(s):
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| readseq Version(s): 1 | Support: Onsite ReadSeq reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences. Machine(s):
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| rosetta++ Version(s): 1 | Support: Corporate The Rosetta++ software focuses on the prediction and design of protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta codes have been repeatedly successful in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition as well as the CAPRI competition and have been modified to address additional aspects of protein design, docking and structure. | |
| rxp Version(s): 1 | Support: Corporate RXP is a validating XML parser written in C. It is used by the LT XML toolkit, and the Festival speech synthesis system. Machine(s):
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| VMD Version(s): 2 | Support: Corporate VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes sourc | |
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