Search Results for "database tool"

Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

AutoMATRIX is a tool to predict key transcription factors in microarray experiments.

ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.

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).

A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.

Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.

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

Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.

Metmask has moved to github http://github.com/hredestig/metmask Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

Venndiagram comparison for ProteinExperiments in the PRIDE Database

Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context

The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.

Evaluation of STICS simulation tool models.

Cyclone aims at facilitating the use of BioCyc, a biological pathway tool. Cyclone provides a comprehensive library of Java classes.

SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging on experience from more than 20 years of information retrieval.

runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.

gbwget is a command line/screen oriented tool to search in nucleotide or protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone.

PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format