Search Results for "java" - Page 13

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.

BioPlatforms Australia (BPA) has funded a number of datasets generation initiatives around important research themes and scientific challenges faced by Australian researchers to provide a unique public resource for the benefit of Australian life sciences research. These large scale genomic, proteomic and metabolomic datasets are being generated and centrally managed by Bioplatforms Australia in collaboration with leading scientists, research institutes and government agencies. With the...

...R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3.

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...

Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.

TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.

SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.

Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and...

Lindenmayer ist ein Programm zur Visualisierung von L- bzw Lindenmayer-Systemen mittels hübscher Baumgrafiken. Die ausführbaren Dateien und Hinweise zum Quellcode finden Sie auf unserer Homepage unter http://lindenmayer.berlios.de/.

Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex

ATOM is an OMERO client which allows automated import of image data into OMERO. ATOM is provided as is without any guarantees or warranty. The author is not responsible for any damage or losses of any kind caused by the use or misuse of the programs.

Screensaver is a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays. It is a Java/JSF/Hibernate/Spring web application that is actively being developed and used at Harvard Medical School. Note: The Screensaver project has moved to GitHub at https://github.com/hmsiccbl/screensaver.

Add-on to Haploview that picks tagSNPs while allowing for: (1) preferential selection based on user-defined criteria, (2) selection across multiple populations, (3) selection outside defined genomic regions, and (4) picking of surrogate (backup) tagSNPs.

A gibbs energy calculator based on the CDK.

A web based application to track protein related reagents including DNA constructs, cell lines, supes, and purified proteins. Supports creating, tracking, and prioritizing requests for transfections and DNA. Includes search and PDF reports.

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.

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 plugin allows automatic highlighting of pathways in an easy and understandable manner.

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.

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.

Shrec is a bioinformatics tool for error correction of HTS read 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