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Showing 93 open source projects for "http"
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Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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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. -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and... -
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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The Comprehensive School Dismissal SolutionPikMyKid is the first and only safe & smart dismissal solution for school districts, charter/private schools, after-school programs, YMCAs, JCCs, Summer camps, and daycare facilities. It connects schools, teachers, and parents through real-time tools to make dismissals safer and more efficient. PikMyKid schools are able to confidently organize their dismissals with ease and no longer rely on paper notes or tedious phone calls to the front office.
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Stanford Data Miner
Tools for integration and analysis of heterogeneous immunological data
An extensive description of this system is published in the Journal of Translational Medicine (http://www.translational-medicine.com/). In brief, the system consists of two main web applications, a data integration app and a data exploration app. The data integration app is a fully custom Java "Web 2.0" product called Sherpa. Sherpa uses Seam, a platform integrating Asynchronous JavaScript and XML (AJAX), JavaServer Faces (JSF), the Java Persistence API (JPA), and Enterprise Java Beans (EJB) 3.0. ... -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . ...
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
...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. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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COHCAP
City of Hope CpG Island Analysis Pipeline
...Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download -
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TIES
A smart search engine for medical documents
...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 maintained, as of 8/15/2019. You are free to continue to use this software under the license for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
...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: http://dx.doi.org/10.1016/j.cmpb.2017.03.010 You can see more information about AntibiogramJ in https://sourceforge.net/p/antibiogramj/wiki/Home/ Several videos explaining the use of AntibiogramJ are available in https://sourceforge.net/p/antibiogramj/wiki/Videos/ AntibiogramJ includes now the EUCAST v.9.0. Please address any question or comment to joheras at gmail.com -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
...The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 . -
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A genome wide mapping data interpretation platform for NGS(ChIPSeq). A tutorial can be found at: http://genomeast.igbmc.fr/wiki/doku.php?id=training:seqminer
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...Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
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...The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). HTDP provides quick filtering functionality and can process data consisting of single or multiple input files. Citation: Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, et al. (2018) High-Throughput Tabular Data Processor – Platform independent graphical tool for processing large data sets. ...
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj -
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NOTE: Use of this codebase is NOT RECOMMENDED. This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code). Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository. Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware. See wiki at https://sourceforge.net/p/jaer/wiki/
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DORY
For mining KASH proteins (SUN domain-interacting proteins)
....*** Please see the following publication for detail: Zhou X, Graumann K, Wirthmueller L, Jones JDG, Meier I (2014) Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants. The Journal of Cell Biology 205(5):677-692. http://jcb.rupress.org/content/205/5/677.full Please see other useful tools for biology research: https://sourceforge.net/projects/cloversystem/?source=directory -
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JBioFramework
Growing suite of proteomics simulations for educational purposes
...Please don't hesitate to review the software below or email Paul Craig [pac8612@rit.edu] with larger descriptions/bugs/feature ideas. Our next scheduled release will contain (in addition to 2DE and MassSpec) a 1D Electrophoresis simulation as well as a tab containing ChemAxon's MarvinSketch [http://www.chemaxon.com/products/marvin/] along with some improved functionality. It should be out shortly as we complete the creation and modification of a permanent domain for the project. -
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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Entrainer is a Java program (JRE 1.8.0_40+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.
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PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
...It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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SILA
Automated bacterial and archaeal genome annotation system
...It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801 -
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...medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0. MedTime is licensed under GNU General Public License version 3.0 (GPLv3). cTAKES development has moved to apache.org. See http://ctakes.apache.org/
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Science & Engineering Inventory
Rediscover the Simplicity http://www.atgclabs.com/
Request new Lab Inventory feature or module and receive a free Single User version with new feature. Help us to improve Lab Inventory. We want to hear your feedback! https://www.atgclabs.com/products/li The Lab Inventory System is an innovative, easy to learn full-featured solution for research laboratories. You can quickly and easily upload your existing Excel based inventory and get started in minutes, manage laboratory inventory, place orders and keep track of them in one...
