Tools   Select Another Resource Report Type

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://github.com/alexlib/KymoButler-1

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

Proper citation: KymoButler (RRID:SCR_021717) Copy   

•   Source: SciCrunch Registry

https://models.physiomeproject.org

Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS.

Proper citation: Physiome Model Repository (RRID:SCR_017374) Copy   

•   Source: SciCrunch Registry

http://www.vasotracker.com

Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system.

Proper citation: VasoTracker (RRID:SCR_017233) Copy   

•   Source: SciCrunch Registry

http://www.ariesepigenomics.org.uk/

Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time.

Proper citation: Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/HicServices/RDMP/wiki

Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.

Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy   

•   Source: SciCrunch Registry

https://github.com/robince/gcmi

Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula.

Proper citation: Gaussian-Copula Mutual Information (GCMI) (RRID:SCR_016450) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.

Proper citation: PALM (RRID:SCR_017029) Copy   

•   Source: SciCrunch Registry

https://www.rappsilberlab.org/software/xisearch/

Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides.

Proper citation: xiSEARCH (RRID:SCR_018395) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@Tracer@v1.6

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

http://flybrain.stanford.edu/

Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.

Proper citation: Flybrain at Stanford (RRID:SCR_001877) Copy   

•   Source: SciCrunch Registry

http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/

A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane.

Proper citation: OME-TIFF Format (RRID:SCR_002636) Copy   

•   Source: SciCrunch Registry

http://www.orcid.org/

Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities.

Proper citation: ORCID - Open Researcher and Contributor ID (RRID:SCR_008700) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/seqgen/

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

Proper citation: Seq-Gen (RRID:SCR_014934) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/ariba

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

Proper citation: Ariba (RRID:SCR_015976) Copy   

•   Source: SciCrunch Registry

http://www.functionalnet.org/humannet/about.html

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

Proper citation: HumanNet (RRID:SCR_016146) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

•   Source: SciCrunch Registry

http://www.genedb.org/Homepage/Lmajor

Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

Proper citation: GeneDB Lmajor (RRID:SCR_004613) Copy   

•   Source: SciCrunch Registry