Search Results for "open source assembly software source code" - Page 5

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...

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l

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

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003

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.

Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)

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.

VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.

A phologenetic supertree construction/assembly tool using triplet similarity as the objective function.

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

This is an independent fork of the ensj-core Ensembl Java API. This version of the API does not receive support from Ensembl. The project is still available under the original LGPL license.

This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

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

GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.

The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

HeliconiusDB is a project to develop a database schema and web-based software tools for the study of Heliconius butterflies (and other organisms) in evolutionary biology.

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

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.