Search Results for "graphical user interface" - Page 3
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Showing 239 open source projects for "graphical user interface"
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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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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PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.
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Library of various Java Swing user interface components, with emphasis on views and editors for complex data structures, like collections, sets, lists, maps, graphs, and matrices.
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merlin is an user-friendly Java application that performs the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools for the...
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877,...
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SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.
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scipion-xmipp
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated... -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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FoodDiary
FoodDiary is an app, that tracks what you have eaten.
FoodDiary is an mobile app, that helps you, tracking what you have eaten in order to stay fit ;). A foodlist is available, that gets updated as often, as possible, and every user has the ability to add and correct data. An activity list is available in order to track, how many calories you have burned. There is also an biodata recording included, that helps tracking your personal goals. -
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
...To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The... -
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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.
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Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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adLIMS
adLIMS: a Laboratory Information Management System with ADempiere
Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the... -
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Coulson Plot Generator
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG. -
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xAffect
Sensor Middleware
xAffect is a software framework for online recording, processing and storage of multi sensor data. It was developed at FZI Research Center for Information Technology, Karlsruhe, Germany. xAffect can be used as a flexible, customizable middleware between physiological sensors and applications which require online feature computation (e.g. biofeedback or affective computing). Moreover, it can also be used as a standalone application for data acquisition and visualization. -
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
...It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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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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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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coalescent
Software tool for Research in Computational Population Genetics
Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT
