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https://www.bio.ifi.lmu.de/software/watchdog/index.html

Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent.

Proper citation: Watchdog (RRID:SCR_018355) Copy   

•   Source: SciCrunch Registry

http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.

Proper citation: DichroWeb (RRID:SCR_018125) Copy   

•   Source: SciCrunch Registry

https://github.com/embl-cba/fiji-plugin-bigDataProcessor/blob/master/README.md

Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.

Proper citation: Big Data Processor (RRID:SCR_018484) Copy   

•   Source: SciCrunch Registry

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) Copy   

•   Source: SciCrunch Registry

https://www.perkinelmer.com/uk/product/harmony-4-8-office-hh17000001

Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems.

Proper citation: Harmony (RRID:SCR_018809) Copy   

•   Source: SciCrunch Registry

http://www.neurostruct.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A built-in toolbox for the tracing and analysis of neuroanatomy from nanoscale (high-resolution) imaging. It is a project under ongoing development. The name is originating by merging the words Neuron + reconstruct. The working concept is organized in filters applied successively on the image stack to be processed (pipeline). Currently, the focus of the software is the extraction of detailed neuroanatomical profiles from nanoscale imaging techniques, such as the Serial Block-Face Scanning Electron Microscopy (SBFSEM). The techniques applied, however, may be used to analyze data from various imaging methods and neuronal versatility. The underlying idea of Neurostruct is the use of slim interfaces/filters allowing an efficient use of new libraries and data streaming. The image processing follows in voxel pipelines by using the CUDA programming model and all filters are programmed in a datasize-independent fashion. Thus Neurostruct exploits efficiency and datasize-independence in an optimal way. Neurostruct is based on the following main principles: * Image processing in voxel pipelines using the general purpose graphics processing units (GPGPU) programming model. * Efficient implementation of these interfaces. Programming model and image streaming that guarantees a minimal performance penalty. * Datasize-independent programming model enabling independence from the processed image stack. * Management of the filters and IO data through shell scripts. The executables (filters) are currently managed through shell scripts. The application focuses currently in the tracing of single-biocytin filled cells using SBFSEM imaging. : * Extraction of neuroanatomical profiles: 3D reconstrution and 1D skeletons of the imaged neuronal structure. * Complete tracing: Recognition of the full neuronal structure using envelope techniques, thereby remedying the problem of spines with thin necks of an internal diameter approaching the SBFSEM resolution. * Separation (Coloring) of subcellular structures: Algorithms for the separation of spines from their root dendritic stem. * Evaluation and analysis of the imaged neuroanatomy: Calculation of the dendritic and spine membrane''s surface, spine density and variation, models of dendrites and spines

Proper citation: Neurostruct (RRID:SCR_008861) Copy   

•   Source: SciCrunch Registry

https://www.brainproducts.com/

Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.

Proper citation: Brain Products (RRID:SCR_009443) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk/psipred/

Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.

Proper citation: PSIPRED (RRID:SCR_010246) Copy   

•   Source: SciCrunch Registry

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

Proper citation: miRDeep (RRID:SCR_010829) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.

Proper citation: Autogrid (RRID:SCR_015982) Copy   

•   Source: SciCrunch Registry

https://github.com/kdmurray91/axe

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

Proper citation: Axe (RRID:SCR_015984) Copy   

•   Source: SciCrunch Registry

https://github.com/pezmaster31/bamtools/wiki

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

Proper citation: Bamtools (RRID:SCR_015987) Copy   

•   Source: SciCrunch Registry

https://github.com/markmikkelsen/Gannet

Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.

Proper citation: Gannet (RRID:SCR_016049) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/SimonHTausch/HiLive

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

Proper citation: HiLive (RRID:SCR_016134) Copy   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://genometools.org

Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.

Proper citation: GenomeTools (RRID:SCR_016120) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE.

Proper citation: loadGtfToGe_db (RRID:SCR_015998) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry