Search Results for "informatics" - Page 17
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Showing 445 open source projects for "informatics"
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A Python interface to the Wordnet database of word meanings and lexical relationships. allows the user to type expressions such as N['dog'], hyponyms(N['dog'][0]), and closure(ADJ['red'], SYNONYM) to query the database for lexical relationships.
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Affymetrix GeneChip Operating Software (GCOS) is used to control Affymetrix Microarray scanners and fluidic stations. Using the DCOM API, this project provides programmatic scripting of GCOS using Python.
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Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.
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SureFit generates 3D mesh surfaces (in VTK and Caret formats) from 3D structural MRI volumes (in formats such as Analyze, AFNI, raw).
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The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.
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Zherlock has now changed name to SciCraft and no longer hosted on sourceforge. Visit our new site at http://www.scicraft.org
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Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
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Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.
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Galileo is a library for developing custom distributed genetic algorithms developed in Python. It provides a robust set of objects that can be used directly or as the basis of derived objects. Its modularity makes it easy to extend the functionality. The
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ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
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jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
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ĄHola!, for "Hordes of Little Atoms," is a project to develop a lean, modular, scalable toolkit for massive simulations of particle (molecular) dynamics. It is written in C and Python to get the best balance between programmer and run time.
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A python library for handling and analyzing biological sequence annotations as described in GFF files (General Feature Format). The library is intended to be a complete framework for this file format.
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FreePM is an opensource physicians practice management / electronic medical record application. The company providing support for FreePM nolonger exists. You may consider TORCH http://sourceforge.net/projects/op-torch/ or one of the other FOSS EMR's.
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DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.
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Hierarchical Stochastic Block Model
just a bunch of PhD projects
Development codes for hierarchical stochastic block models -
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malty_DEPRECATED
translates alignments of A-to-B and B-to-C to A-to-C; has BAM support
Development moved to: https://bitbucket.org/rongchenlab/malty Docs moved to: http://malty.readthedocs.org/en/latest/ -
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The RNA Ontology Consortium proposed a translation the RNA backbone angles to 46 clusters ('suites') and hence unique names. This project calculates the suites from RNA 3D structures, and to search on a Java-based index structure of known folds.
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pymzML
Python module to interface mzML data in Python
Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics. CITATION Please cite us when using pymzML for your publications. Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., & Fufezan, C. (2012). pymzML - Python module for high throughput bioinformatics on mass spectrometry data. Bioinformatics, 1-2. doi: 10.1093/bioinformatics/bts066 -
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MePrId is a Python program which can be used to classify a protein, depending whether it is a membrane or a globular protein. Download link: http://meprid.svn.sourceforge.net/viewvc/meprid.tar.gz?view=tar