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Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
The Fortran program MOLLY generates atomic positions in a molecule from those of a small number of prototype atoms and the molecule's point symmetry. It is intended as a time-saving aid in preparing input data for computational physics software.
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SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.
primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.
The Blue Obelisk is a group of scientists driven by a belief in Open Source, Open Standards and Open Data, expressed in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across.
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Develop a basic understanding of the behavior of polar spherical coordinates through selected examples. Provide sample files for diverse mathematics engines
Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.
ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.
NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.
The C Protein Folding Library is a minimalistic, high-performance modular library of C functions and data structures for computing folding simulations of proteins on a wide variety of computer hardware.
Datagam is a tool for extracting data from output or punch files produced by GAMESS(US) or FireFly (old name PC GAMESS) packages. Mac GUI wrapper also available.
Upstream version of the project goes to the launchpad. Only final versions of the source code and compiled binars will be available from this domain.
QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.
Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
IMP is an automated tool for intron-flanking primer design based off of Expressed Sequence Tags (ESTs). It's intended for use in species with limited to no genomic sequence data available.
A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
WebBabel is a python web application using OpenBabel to convert files
from one format to another.
It runs under Windows, Mac or Linux on your desktop, workstation or laptop.
It uses the Jmol (or Marvin) viewer to show the structures being converted.