Search Results for "oracle-apex-workflow" - Page 2

The SeqSelector toolset is a suite of user-friendly, platform independent python scripts to facilitate selection of sequences for targeted enrichment of next-generation libraries through hybridization-based sequence capture. The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. Once a list of candidate genes has been identified, their sequences are selected from the reference genome. These sequences are used as a query during a BLAST search of the unannotated genome of a non-model species, and then the corresponding sequences are returned, which can be used to design baits for hybridization-based sequence capture.

Ergatis is a web-based utility used to create, run, and monitor reusable computational analysis pipelines, utilizing the Workflow engine. It contains pre-built components for common bioinformatics analysis tasks.

The iBRAIN2 software system for RNAi high-content screening integrates automated analysis and customizable data management. It enables robust and complex parallel processing on computer cluster infrastructure and allows for reliable storage of primary and resulting data sets.

Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time.

ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML).

Open source code base for enabling software innovation in imaging. The extensible and robust platform includes viewing, archiving, management, workflow and distribution of images as well as an open architecture for core competency tool development.

Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror hosted at the University of Queensland. ...

A R based universal workflow for analysising miRNA sequencing data

Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.

ProPHAnE: Proteomics result Pruning and Homology group Annotation Engine A perl script based workflow for annotation of protein data coming from the 'Mascot' (Matrix Science) and 'Scaffold' (Proteome Software) pipeline. Coming soon: Prophane 2, "a much improved and extended version of Prophane based on HTML5, PHP and MySQL. Most importantly, the pipeline includes now functional predictions on profile Hidden Markov models (HMMs), is fully-automated, and can be controlled via a highly intuitive and user-friendly interface." ...

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.

Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.

A software solution for clustering large EST/mRNAs datasets.

Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.

ChromEval allows rapid assessment of HPLC performance using visual and quantitative metrics for quality control runs interspersed among a regular LC-MS workflow.

OpenClinica is a web-based electronic data capture platform for clinical research. See http://www.OpenClinica.org/ for downloads, documentation, and mailing lists.

BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.

Care4G is a web-based software, as forking of the most famous care2x, it will be a complete HIS for the II Millennium...

Taverna is *no longer* hosted on SourceForge, but has moved to the Apache Software Foundation: https://taverna.apache.org These pages and mailing list archives are provided for *archival purposes* for older Taverna 1.x releases. See https://taverna.apache.org/download/ for the latest releases from Apache Taverna.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.

Cyrille is an workflow management system aimed at high throughput pipelines in Bioinformatics.

http://ewi.utwente.nl/~biorange/rshell - The RShell project is a plugin for the Taverna workflow system. It enables one to execute R scripts within the Taverna workflow system. The RShell processor is built on the RServe project. For more info:

Multiomics Information Management and Annotation System (MIMAS)

The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers