Search Results for "alpha" - Page 3

The objective of this project is to make available an open-source of a gridified version of the Multifactor Dimensionality Reduction (MDR) software (http://www.epistasis.org/software.html).

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

BioX (pronounce as bio cross) is a system for the management of local and remote (currently supporting RMI, CORBA and SOAP Web Services) components such as files and services (e.g. BLAST). Additionally, the components can be composed to workflows.

CB-Commander is a plugin based tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface.

Data curation tool to maintain variables for the National Survey of Health and Development managed by the Lifelong Health and Ageing Unit of the Medical Research Council.

SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk

Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

Contemplate is a bioinformatics tool for finding cis-regulatory modules (CRMs) in noncoding genomic regions using comparative sequence data.

Software environment for manipulation of DNA and protein sequences in a phylogenetic context.

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

Java forward population genetics simulation tool similar to 'ms'

Reference compression tools for sequence read data.

SRMA is a post-alignment micro re-aligner for next-generation high throughput sequencing data.

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.

JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.

An open source MAGE-TAB database and import/export tools to read and write MAGE-TAB formatted data. MOLGENIS is being used to autogenerate it. Import/export tools creation is in progress.

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.

Small set of utilities used by the 2010 iGEM Mexico-UNAM-CINVESTAV Team to automate biobricks from files

DIVAT (Diagnostic Immunohistochemistry Visualization and Analysis Tool) is designed to graphically analyse comprehensive data sets of immunohistochemical results as those used in clinical diagnostic pathology.

FAS-DPD is a program to design degenerate primers for PCR.

This is a java open source package for analyzing bio-data. We build this project as an inititive for people interested in bio-informatic to share new ideas and publish their innovative methods.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.