Search Results for "research" - Page 19
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Showing 2679 open source projects for "research"
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The MCISB Project contains software solutions developed in the Manchester Centre for Integrative Systems Biology, University of Manchester.
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Program jobman (Job Manager) glues executables written in different languages according to a given flow. The program can run executables with arguments in parallel (multiprocessed) or in loop or in any combination of them.
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KneeTex is an open–source, stand–alone application for information extraction from narrative reports that describe an MRI scan of the knee. Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects. The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions. As a result, formally structured and coded information allows for complex...
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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Logic Calculator
A Calculator to perform logical operations
The Logic Calculator is an application useful to perform logical operations. It has three modes: (1) Evaluation of logic formulae: In this mode we have the basic boolean operations (negation, conjunction, disjunction, conditional and biconditional) so the user can insert the logic formula and the Logic Calculator displays the truth table along with the models of the formula. (2) Logical entailment: In this mode the user can insert a number of premises followed by a number of... -
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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JConvert is a free unit conversion program that has a friendly user interface and can also be used with external applications. Conversions can be modified and/or added easily. Supports multiple languages. Downloads and runs in seconds! Try it now.
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Host LLMs in Production With On-Demand GPUsDeploy your model, get an endpoint, pay only for compute time. No GPU provisioning or infrastructure management required.
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jAgg
jAgg - Java Aggregation Operations
jAgg is a Java 5.0 API that supports “group by” operations on Lists of Java objects: aggregate operations such as count, sum, max, min, avg, and many more. It supports Super Aggregation: Rollups, Cube, and Grouping Sets. It supports analytic operations such as lag/lead and row number and more. It also allows custom aggregate and analytic operations. -
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S2O
Converting IBM SPSS files to CDISC ODM
This tool can be used to convert data collections based on IBM SPSS Statistics to the data standard for definition and exchange of clinical trials: CDISC ODM (Operational Data Model). Possible use-cases: - A project is running out of funding and scientific data collection should be performed in free available/open-source data capture systems - Advantages of reliable EDC systems like: Data security (role/right management), backup infrastructure, support of the entire clinical trial... -
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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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This is a parser in Java for Lisp S-expressions. An S-expression or sexp (for symbolic expression) is a convention for representing data using parentheses.
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The bflow* Toolbox is an open source tool kit for business process management. The objective of bflow* is to explore new ways and scenarios for the development and use of modelling tools.
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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EXMARaLDA stands for "Extensible Markup Language for Discourse Annotation". It's a system of concepts, data formats and tools for the computer assisted transcription and annotation of spoken language, and the analysis of spoken language corpora. This project's source code has moved to https://github.com/Exmaralda-Org/exmaralda
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ThreadPoolTester
Performance Testing Tool For Thread Pool Systems
ThreadPoolTester is a performance testing and comparison tool for java based Thread Pools. -
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mathCollection is a java package representing a consistent and efficient extension to the Java Collection Framework of JDK 1.4. It offers different kinds of sets with mathematical, non-destructive functions.
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Universal Java Matrix Package
sparse and dense matrix, linear algebra, visualization, big data
The Universal Java Matrix Package (UJMP) is an open source Java library which provides sparse and dense matrix classes, as well as a large number of calculations for linear algebra such as matrix multiplication or matrix inverse. Operations such as mean, correlation, standard deviation, replacement of missing values or the calculation of mutual information are supported, too. The Universal Java Matrix Package provides various visualization methods, import and export filters for a large... -
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safecap
Safecap Platform for improving railway capacity via formal modelling
The overall aim of the SafeCap project is to develop modelling techniques and tools for improving railway capacity while ensuring that safety standards are maintained. Useful links: Project homepage: http://http://safecap.co.uk/ -
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Implementation of an OGC Web Map Service, primarily for serving images dynamically generated from NetCDF data files (although other file formats can also be handled). Also an AJAX web mapping interface based on OpenLayers.
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StreamAID
A framework for prototyping and testing P2P live streaming algorithms
StreamAID facilitates fast prototyping of P2P live algorithms that can be built in a modular approach. -
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Virmid
Virtual Microdissection for SNP calling
NEWS: 11-07-2013 A new version Virmid 1.1.0 has been uploaded. 08-29-2013 Virmid paper is now published in Genome Biology. Kim S et al, "Virmid: accurate detection of somatic mutations with sample impurity inference", Genome Biology 2013, 14:R90 http://genomebiology.com/2013/14/8/R90/abstract Virmid (Virtual Microdissection for SNP calling) is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within... -
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An API for manipulating EDIF netlists in Java. We use this API to analyze netlists as a part of our FPGA reliability project. We intend to keep the API as general as possible to support other netlist analysis and manipulation activities. This material is based upon work supported by the National Science Foundation under Grant No. 0801876. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the...
