Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.
Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.
OpenAlea is a modeling and simulation framework in plant ecophysiology. It is based on the Python programming language and it provides different integration tools (for tasks such as installation and compilation), a visual programming interface, and different dedicated models and libraries.
This package contains Virtual Hybridization tools. Virtual Hybridization uses sets of short probes to generate datasets for comparative genomics: given a DNA sequence and a set of probes, the typical output will give a sequence of oriented probe hits along the DNA sequence. Other tools are supplied to allow simple manipulations such as format conversion and extraction of permutations.
Pipviewer is a visualizer for multiple alignments of genomic sequences. It highlights conserved regions and allows basic annotations. Its main goal is to find conserved probes for the construction of gene order data sets. Selected regions marked as 'probes' can be exported to fasta format. It can also retrieve gene annotations from the NBCI and display this information along the alignment. Pipviewer is not an aligner. You must compute the alignment with another tool like Clustal or Multi PIP Maker.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.