Open Source Java Bio-Informatics Software - Page 34

Information System "Supercritical Fluid Extraction" has developed as tool for collecting and analyzing the experimental data from various supercritical fluids experiments. The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk).

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

NOTE: Use of this codebase is NOT RECOMMENDED. This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code). Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository. Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware. See wiki at https://sourceforge.net/p/jaer/wiki/

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

jTerm is a light-weight platform independent vocabulary/terminology server. It support multiple terminologies using an abstract model. The system is provided as a J2EE deployable application supporting a web frontend for navigation of the terminologies.

JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).

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.

Java forward population genetics simulation tool similar to 'ms'

LocusVu is a novel Java based software tool that accepts a list of genomic loci (positions on the chromosome) as input and automates fetching of related information (cytogenetic band, gene name, OMIM data etc.) from public databases such as the UCSC genome browser database. It then enables multiple workflows on the retrieved results, like comparing multiple datasets (comparative genomics), viewing neighboring genes for a loci from within the tool itself, or graphically representing these results in bar / pie charts. LocusVu has a simple easy-to-use GUI on the frontend which enables intuitive user interaction with the underlying logic. The tool can be easily extended to add support for other databases (eg. Ensembl) or to fetch information from other tables in the database. Thus, LocusVu provides a basic framework that can be used by users and developers alike in simplifying existing workflows and creating newer ones to support data analysis in genomics.

Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.

Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need to be differentiated is high. One extremely useful but underused method for this purpose is the multiplex pyrosequencing technique. mPSQed is a program developed at the Robert Koch Institute and targeted at facilitating the creation of such assays.

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.

MARSHAL (Managing Additional References in Short-Read Alignment) enables short-read nucleotide sequence aligners to simultaneously analyze multiple references, facilitating the detection of structural variation.

The MCISB Project contains software solutions developed in the Manchester Centre for Integrative Systems Biology, University of Manchester.

Memomics Forge is a meta-project for software that utilizes the Memomics Semantic Service. Memomics Semantic Service provides semantic data which can be embedded in applications via webservices.

merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools for the compartmentation of the model that predict the localisation of the proteins encoded in the genome, and thus the localisation of the metabolites involved in the reactions induced by such proteins. Finally, merlin expedites the transition from genome-scale data to SBML metabolic models, allowing the user to have a preliminary view of the biochemical network.

The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R, TegetMeyer H (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Frontiers in Microbial Physiology and Metabolism 3:410. doi: 10.3389/fmicb.2012.00410

Graphically visualize 1 dimensional data.

A small java API library for running the MM3 molecular mechanics package from within a java environment. It does not include MM3, nor implement MM3. The MM3 binaries have to be available on the user system.

Moara is a biological text mining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.

The library allows to communicate with BioMOBY Registries and implements all operations such as retrieval, search, registration, deregistration of services, data types etc...