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http://www.nitrc.org/projects/abcdrepronim/

Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.

Proper citation: ABCD-ReproNim Course (RRID:SCR_018911) Copy   

•   Source: SciCrunch Registry

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry

https://github.com/HicServices/BadMedicine

Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes.

Proper citation: BadMedicine (RRID:SCR_018879) Copy   

•   Source: SciCrunch Registry

https://mcguinlu.shinyapps.io/robvis/

Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project.

Proper citation: robvis (RRID:SCR_018755) Copy   

•   Source: SciCrunch Registry

https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-imager-2-for-life-science-research.html

Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software.

Proper citation: Zeiss: Axio Imager 2 (RRID:SCR_018876) Copy   

•   Source: SciCrunch Registry

https://www.t2dsystems.eu/t2dsystems

Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.

Proper citation: T2DSystems (RRID:SCR_018913) Copy   

•   Source: SciCrunch Registry

http://diabeticfootconsortium.org/

Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.

Proper citation: Diabetic Foot Consortium (RRID:SCR_018914) Copy   

•   Source: SciCrunch Registry

https://github.com/ylab-hi/ScanITD

Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation.

Proper citation: ScanITD (RRID:SCR_018886) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

http://www.cgga.org.cn/

Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype.

Proper citation: Chinese Glioma Genome Atlas (RRID:SCR_018802) Copy   

•   Source: SciCrunch Registry

http://faculty.ucr.edu/~mmaduro/random.htm

Web application to generate random DNA sequences.

Proper citation: Random DNA Sequence Generator (RRID:SCR_018768) Copy   

•   Source: SciCrunch Registry

https://github.com/davidebolo1993/TRiCoLOR

Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments.

Proper citation: TRiCoLOR (RRID:SCR_018801) Copy   

•   Source: SciCrunch Registry

https://neurophysics.ucsd.edu/Manuals/Master%208/Master%208%20Eight%20Channel%20Programmable%20Pulse%20Generator.pdf

Pulse generator that can hold 8 different pre-programmed paradigms all of which can use up to all 8 channels.

Proper citation: A.M.P.I.: Master 8 stimulator (RRID:SCR_018889) Copy   

•   Source: SciCrunch Registry

https://beikolab.cs.dal.ca/software/STAMP

Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups.

Proper citation: STAMP (RRID:SCR_018887) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

https://www.coleparmer.in/i/masterflex-l-s-variable-speed-digital-drive-with-remote-i-o-6-to-600-rpm-90-to-260-vac/0752810

Peristaltic pump with flow rate 0.06 to 3400 mL/min, three digit LED display, reversible motor, LED indicators to confirm motor direction and speed range from 6 to 600 rpm.

Proper citation: Cole-Parmer: Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump (RRID:SCR_019028) Copy   

•   Source: SciCrunch Registry

http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/

Software Matlab toolbox to perform representational similarity analysis for neural data.

Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy   

•   Source: SciCrunch Registry

https://ihg.gsf.de/ihg/mitoprot.html

Web server for prediction of mitochondrial targeting sequences.

Proper citation: Mitoprot (RRID:SCR_019023) Copy   

•   Source: SciCrunch Registry

http://genometools.org/

Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs.

Proper citation: LTRharvest (RRID:SCR_018970) Copy   

•   Source: SciCrunch Registry

https://zlab.bio/guide-design-resources

Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020.

Proper citation: Guide Design Resources (RRID:SCR_018982) Copy   

•   Source: SciCrunch Registry