Search Results for "quickfix/j - open source java fix engine"
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Showing 28 open source projects for "quickfix/j - open source java fix engine"
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OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. OpenClinic GA and OpenClinic GMAO are owned by Frank Verbeke, MD, PhD at Post-Factum BV (https://www.post-factum.be) -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. ... -
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SequestGUI
GUI front-end to sequest.exe
GUI front-end to sequest.exe proteomics search engine, developed in Perl. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/sequestgui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. -
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OmssaGUI
GUI front-end for OMSSA
GUI front-end for the OMSSA proteomics search engine. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/omssagui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer... -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
AntibiogramJ is a Java program for the identification, measurement and categorisation of inhibition zones in antibiogram images captured with any device that incorporates a camera (including digital cameras and mobile phones). Citing AntibiogramJ: A. Alonso, C. Domínguez, J. Heras, E. Mata, V. Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI:... -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)
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scFvMiner
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. New... -
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BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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Fylogenetica
Constructing level-1-networks consistent with a set of quartets
This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets. -
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SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
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An api for domain level interaction with SNOMED CT and an implementation based on a storage engine using a native SNOMED distribution stored in neo4j as a backend.
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The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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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.
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Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
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A wrapper that makes the UMLS MetaMap tool (http://mmtx.nlm.nih.gov/) available as an UIMA analysis engine.
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This project develops a web-based (JSP) Fuzzy Rule-Based Expert System for analyzing ECG (electro cardio gram) signals & diagnosing Tachi-Arrhythmias. Proj. main blocks: inference engine, knowledgebase, KB editor, explanation, and feature extraction.
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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.
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
