Search Results for "gnu science" - Page 9

A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.

defunct

Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

Rana, Restriction Analysis Libraries. Rana is written in Python and provides a set of libraries and scripts to work with restriction enzymes and ADN. The aim is to ease the development of molecular biology software for research or education purposes.

defunct

SureFit generates 3D mesh surfaces (in VTK and Caret formats) from 3D structural MRI volumes (in formats such as Analyze, AFNI, raw).

Zherlock has now changed name to SciCraft and no longer hosted on sourceforge. Visit our new site at http://www.scicraft.org

Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.

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

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.

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

generic makefiles for use in bioinformatics

CCPNGrid is a Plone add-on to create a web portal which intends to provide the scientific NMR community with the means to process, analyse and execute advanced 3D-structure calculation and validation software all in a straightforward and simple way.

The aim of our programm is to help lab on counting species and analyze the results with statistics tools.

This software screens a given peak list against web based NMR databases (nmrshiftdb, HMDB...) and return possible molecules. It also take a given molecule to return expected peaks list.

It is a Cross Language Interface Platform that allows different languages to call and execute functions of other languages using xml-rpc as the remote procedure call vehicle.

CC8Works is a Web-based software system for managing and documenting a cross of eight existing inbred mouse lines to yield hundreds to thousands of recombinant inbred lines that will become a permanent genetic resource for biomedical research.

Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.

SpikeyTree infers divergence times between populations that share a common history described by a tree. SpikeyTree assumes that the populations have been evolving under isolation, according to the Wright-Fisher with pure drift. SpikeyTree can use the Beta or the Beta with Spikes approximation to the allele frequency distribution under the Wright-Fisher. More details can be found in Tataru et al. Inference under a Wright-Fisher model using an accurate beta approximation If using...

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

This project seeks to integrate knowledge, methods and data from various disciplines through the design and implementation of a system that allows for communications between languages and different platforms.

Python program devoted to study the relationship between cells during inmune response. It is based on a 3D periodic boundary conditions grid where cells see each other and react according to certain movement, growth and interaction rules.

trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment. trimAl implements a series of...