Open Source Java Bio-Informatics Software - Page 21

Program described in the paper: MUDE: A new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification, 2010. By Cerqueira, Fabio; Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.

MZ-Analyzer is a tool for visualization and analysing of multiple mass spectrometry data in 2D and 3D mode, including the function of quantitating the LC-peak of the specified identified peptides.

SOMMS is an analysis program for mass spectra intended for bio-informatics research. Its goal is to relate theoretical spectra with raw data. A previous version, accompanying an article published in Rapid Comm. in Mass Spectrometry, was written in Perl.

Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.

MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing.

Mars Eva Computing Environment is a JMF, JINI project that is used to provide a collaborative mission planning & execution environment for furture teams on Mars. This effort is part of a simulation for the Mars Society of Australia.

Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.

Matchup program can be used to find universal primers and group-specific probes for DNA-based detection methods llike AFLP(Amplification fragment length polymorphism) or Microarray experiment.

Create custom substitution matrices for BLAST protein search. Easy to use GUI based application.

Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.

Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutit

cTAKES is a system for annotating clinical documents, built on the Apache UIMA framework . cTAKES development has moved to apache.org. Please see http:/ctakes.apache.org

A medical information system for Windows-based systems (95-XP/CE/PocketPC) based on Open Source platforms

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

A wrapper that makes the UMLS MetaMap tool (http://mmtx.nlm.nih.gov/) available as an UIMA analysis engine.

MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-techniques and covers structures and reference spectra as well as biological roles, locations and concentrations.

A computational tool to design and annotate metabolic pathways from genome annotations

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

This project will develop cross-platform Java software for interfacing with EEG devices, specifically hardware developed by the OpenEEG project (http://openeeg.sourceforge.net/).

MirkE is a platform-independent Java application using Hibernate, HSQLDB and Colt designed to facilitate common but tedious calculations on spectrophotometric and colormetric data for molecular and cellular biology assays.

A straight-forward Java implementation of a mixture model with pluggable mixture functions, e.g. a mixture of Gaussian functions. The number and dimensionality of the mixture functions is not limited. All critical calculations are performed in log-space.

Bioinformatics is commonly understood as work with the DNA and protein sequences. However databases and computational analysis were tried on other objects far before these sequences became widely available. This work is about analysis of spatial movement

The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.

MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE.