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.
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.
ESP is a secure, automated system that analyzes electronic medical record (EMR) data to identify and report patients with notifiable diseases to the Massachusetts Department of Public Health. The growing use of electronic medical record systems (EMRs) permits efficient re-use of data already being collected by clinicians during routine private practice, offering an unparalleled opportunity to improve public health practice. Information held in EMR systems includes diagnoses, procedures, laboratory test, and treatment information, as well as patient demographic data. This software permits secure, simple, and robust messaging from electronic medical record systems to public health authorities.
GNUmed is a comprehensive scalable software solution for electronic medical practices with an emphasis on privacy protection, secure patient centric record sharing, decision support, and ease of use. It is intended to become a sophisticated decision support system that will elevate the quality of medical care that can be delivered.
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.
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.