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.
OIO is a Web-based metadata/data management front-end which is built using Zope and works with Postgresql. No programming is required to build and manage Web-forms or to perform data mining/analysis on the collected data. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.
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.
GNotary is a set of Python scripts that implement an asynchronous digital notary service. Anybody who needs certification of any digital document creates a message digest (like MD5 or RIPEMD160) of that document and submits it to the GNotary service by email. GNotary signs this email digitally (using GnuPG), retains a copy of the certified and time stamped message, and mails it back to the sender, optionally with the public key attached to allow the sender to verify the signed document. At regular intervals, the GNotary server creates message digests of its own logs and distributes them among other GNotary servers, thus making it virtually impossible to forge the chain of evidence that authenticates a submitted document.
The GNotary client is a multi-platform GUI client that allows you to select files via drag and drop from any file manager, create the secure hash sums for each file, and submit the hash list to a list of digital notary servers. Optionally, all selected files can be backed up into a zip archive. It is written in Python and requires the wxPython toolkit.
Devices for the measurement of signals use different data formats to store the data on disk. libRASCH provides a common application programming interface to access such signals, regardless of which storage format is used. Additionally, it provides support for processing (e.g. detects beats in an ECG) and viewing the signals. This functionality and the access to the various file formats is realized with plugins.
Drugref is a collaborative effort to create and maintain a database of pharmaceutical reference information, tagged by language, country, and reference source. A Web interface written in PHP4 allows the community of health professionals to maintain and review content. The database structure, implemented in PostgreSQL, is designed to facilitate automated decision support. "Tagging" allows one to import information from any source in parallel, thus allowing drugref to work as a generic interface to any kind of (comercially or freely) available drug reference information.
CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.