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Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
https://www.mesquiteproject.org/
Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed.
Proper citation: Mesquite (RRID:SCR_017994) Copy
https://github.com/TomSexton00/4See
Software tool to visualize 4C data.
Proper citation: 4See (RRID:SCR_018014) Copy
https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Proper citation: NeuroChaT (RRID:SCR_018020) Copy
https://github.com/hangyabalazs/opeth
Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.
Proper citation: Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) Copy
https://github.com/hariszaf/pema
Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.
Proper citation: PEMA (RRID:SCR_017676) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
http://metavelvet.dna.bio.keio.ac.jp/
Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.
Proper citation: MetaVelvet (RRID:SCR_011915) Copy
http://omics.informatics.indiana.edu/GeneStitch/
Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.
Proper citation: GeneStitch (RRID:SCR_011910) Copy
A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.
Proper citation: METAREP (RRID:SCR_011926) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://pages.cs.wisc.edu/~bsettles/abner/
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Proper citation: ABNER (RRID:SCR_011868) Copy
http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.
Proper citation: LitInspector (RRID:SCR_011870) Copy
An open-source program for doing molecular docking.
Proper citation: AutoDock Vina (RRID:SCR_011958) Copy
http://cran.r-project.org/web/packages/vegan/index.html
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Proper citation: vegan (RRID:SCR_011950) Copy
Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.
Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy
http://scalpel.sourceforge.net/
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
Proper citation: Scalpel (RRID:SCR_012107) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
