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Specify is a biological collections and species occurrence database management platform for zoological museums, herbaria and other biodiversity specimen repositories. Specify is supported by grants from the Division of Biological Infrastructure, U.S. National Science Foundation and the State of Kansas. A web browser application, Specify 7, is available on GitHub. In 2015, 450 biological collections worldwide use Specify Software for collections data management. An iPad app, Specify Insight...
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section.
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
mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more
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tigreBrowser is a web-based browser for ranking results from R/Bioconductor package tigre and similar tools. It allows easy viewing, sorting and filtering of visualisations of models produced by tigre.
Clover is a simple lab information management system (LIMS) designed for biology labs, especially plant biology labs. It provides an easy way to manage and handle the information of lab material, catalogs (inventories), and orders.
USE PHP 5.*!
Clover will not work on PHP 7.*!
The wiki page contains detailed help documents: https://sourceforge.net/p/cloversystem/wiki/Home/
For lab instrument scheduling, please use Cloveriver:
https://sourceforge.net/projects/cloveriver/
Please...
Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS)
peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/).
iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers.
For more details about iPiG and it's functionallity, please...
VI Compute Server (VICS) is a collection of grid-enabled bioinformatics tools with HTTP (browser) and Web Services (scriptable) interfaces. JCVI VICS is licensed under the Perl Foundation Artistic License 2.0.
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CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.
Stratos viewer is a web based utility to examine DICOM medical images through a web browser.
This project is not active anymore. If you are interested in a Dicom web viewer, have a look at our new development: MedView [ https://github.com/jap1968/medview ]
The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.
A web based tool that combines automatic extraction of gene and protein entities with manual curation done by the researchers who read and write the biomedical texts. The interface is loaded in web browser extensions and viewed along with the abstract.
Shred is a fast and scalable faceted data browser. The application allows users to navigate the data in an intuitive way and by any path they wish to take. Immediate intuitive information regarding the data is apparent.