Search Results for "web-based"
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Showing 35 open source projects for "web-based"
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. ... -
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SBW (Systems Biology Workbench)
Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. -
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.
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DigiOz .NET Portal
ASP.NET MVC Based Portal CMS System to Create an Instant Website
DigiOz .NET Portal is a FREE web based portal CMS system written in ASP.NET MVC 5 in C# which uses a Microsoft SQL Database to allows webmasters to setup and customize an instant website for either business or personal use. List of Technologies used: - ASP.NET MVC 5 - Microsoft SQL Server - Bootstrap - HTML 5 - jQuery Demo Site: http://digioznetportal.digioz.net/ Source Code: https://sourceforge.net/p/digioznetportal/codenew/ci/master/tree/ Installation Instructions: https://sourceforge.net/p/digioznetportal/wiki/Home/ Help Wanted: If you are a developer, and wish to join the project, please email us at support@digioz.com. -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The profile is obtained by calculating the genome-wide Pearson correlation coefficient (R) between the genomic variable values and the TSS (or TTS) counts at incremental shifting of transcribed strand. The data of TSS and TTS counts used to compute the profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting R values for the various shifts of variable coordinates with respect to TSS or TTS. R related to each strand is also reported to verify that a similar profile is obtained in the two direction of transcription. 1) V. Pelechano, W. Wei, L.M. ... -
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CognitionMaster
object-based image analysis framework
Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34 -
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RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
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The Systems Biology Results Markup Language is a language describing data. Unlike flat data formats, SBRML allows describing the origin of the data as well. This project hosts a library and tools for using SBRML.
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Morpheus search algorithm
a mass spectrometry–based proteomics database search algorithm
Morpheus is a mass spectrometry–based proteomics database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. -
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Insulin IP Calc
Insulin infusion protocol calculator
A simple, point of care, clinic decision support system (CDSS) Android app for Insulin infusion and hyperglycemia management in the ICU. The infusion protocol calculator is based on the updated "Yale Insulin Infusion Protocol" http://bit.ly/1DaVfUd and American Association of Clinical Endocrinologists (AACE) blood sugar targets. http://inpatient.aace.com/ . Source code requires Xamarin Studio & Android SDK to compile. -
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CS Miner
A tool for Navigating in Chemical Space
CS-Miner stands for Chemical Space Miner and is a software tool for navigating in chemical space of compound databases. It helps for deriving appropriate classification models and performing virtual screening. Download it via: http://csminer.com/csm/?p=7 A quick tutorial is available through: http://csminer.com/csm/?p=8 -
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PeptideManager_LRNO
Unique Peptide Sequence Finder (host background (xenografts) friendly)
PeptideManager is aimed to help the pre-selection of unique peptide sequences for the design of targeted proteomics approaches. Its main advantage is to allow the presence of a host/background proteome (e.g., xenograft samples) during this peptide sequences selection. PeptideManager can build peptide sequences databases from various public repository (SwissProt/Trembl/UniProt, RefSeq, IPI) and various proteases. For any use, please refer to the publication: doi:... -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are... -
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compare-results
Program comparing Simulation Results for the SBML TestSuite
Compare SBML Test Suite Results =============================== The [SBML Testsuite](http://sbml.org/Facilities/Online_SBML_Test_Suite) allows developers of ODE based simulators to test their implementation against a large number of test cases that test a wide aspect of the [SBML Specifications](http://sbml.org/Documents/Specifications). While implementing my simulator [RoadRunner](http://roadrunner.sf.net) I wanted to be able to compare it using a wider range of parameters: - filter for new tests - filter for tests with specific tags - mark elements that I know I did not implement -
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ClearCanvas
Open source DICOM and RIS/PACS informatics platform
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. -
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OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
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CPC Tools is a collection of open-source proteomics tools for use with mass spectrometry-based proteomics data sets. These tools were created by the Cardiovascular Proteomics Center of Boston University School of Medicine (Boston, MA). STRAP (Software Tool for Rapid Annotation of Proteins) automatically annotates a protein list with information that helps to interpret mass spectrometry data. For more information about STRAP or to download the program, please visit http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/. ...
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a DNA search engine based on statistical n-gram segment and lucene.net. a paper: http://arxiv.org/abs/1006.4114
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STR miner(or SSRdigger) is a SSR searching software which supports both perfect and imperfect SSR search with specified length, match percentage and repeat threshold. With a GUI interface, fasta and MS excel format output, STR miner is user-friendly.
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LSG is a Windows application framework designed for visual data integration and based on Microsoft .NET 2.0 and CAB. An admin utility manages LSG apps, modules, events, and services, and a client integrates the modules and provides functionality hooks.
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This is a mathematical/informatical/biologocal aproach to System-research. The aim is to write a progrramm that simulates a world with as many mathematical methods as possible at once.
