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.
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.
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.
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.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
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.
AntFlow builds upon Apache Ant to provide a new approach to simplifying system automation that uses pipelines of hot folders chained together to perform a given task. Using XML, it associates an automated task such as data transfer, encryption, or XML processing with a directory on the local system. Whenever a file is copied or written into the hot folder, the associated task is executed and the file is moved to the next hot folder in the pipeline for further processing.