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http://www.ucl.ac.uk/ploras#annotations:QXuC2C7REeaxtw-aEPo07Q
A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others.
Proper citation: Predicting Language Outcome and Recovery After Stroke (PLORAS) (RRID:SCR_014498) Copy
http://www.virtualflybrain.org
An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.
Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy
http://caps.ncbs.res.in/imotdb/
Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members.
Proper citation: Database of Spatially Interacting Motifs in Proteins (RRID:SCR_007735) Copy
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
http://www.imperial.ac.uk/research/animallectins
Resource presents information about animal lectins involved in various sugar recognition processes.
Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy
http://www.opensourcebrain.org
A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.
Proper citation: Open Source Brain (RRID:SCR_001393) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
http://bioconductor.org/packages/release/bioc/html/SC3.html
Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
Proper citation: SC3 (RRID:SCR_015953) Copy
https://github.com/neurodroid/stimfit
Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.
Proper citation: Stimfit (RRID:SCR_016050) Copy
http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
Proper citation: Clonalframe (RRID:SCR_016060) Copy
https://sanger-pathogens.github.io/gubbins/
Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Gubbins (RRID:SCR_016131) Copy
Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.
Proper citation: Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) Copy
http://www.compbio.dundee.ac.uk/jpred/
Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.
Proper citation: Jpred (RRID:SCR_016504) Copy
https://github.com/LabTranslationalArchitectomics/RiboWaltz
Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.
Proper citation: riboWaltz (RRID:SCR_016948) Copy
http://shiny.chemgrid.org/boxplotr/
Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.
Proper citation: BoxPlotR (RRID:SCR_015629) Copy
http://enterobase.warwick.ac.uk/
Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.
Proper citation: EnteroBase (RRID:SCR_019019) Copy
Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.
Proper citation: xiNET (RRID:SCR_021010) Copy
http://www.compbio.dundee.ac.uk/gotcha/gotcha.php
GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool
Proper citation: GOtcha (RRID:SCR_005790) Copy
http://www.ebi.ac.uk/expressionprofiler/
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.
Proper citation: Expression Profiler (RRID:SCR_005821) Copy
Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.
Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy
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