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https://biosimulators.org

Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects.

Proper citation: BioSimulators (RRID:SCR_019111) Copy   

•   Source: SciCrunch Registry

https://github.com/bgcarlisle/Numbat

Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context.

Proper citation: Numbat (RRID:SCR_019207) Copy   

•   Source: SciCrunch Registry

https://usdrn.org/

Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.

Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy   

•   Source: SciCrunch Registry

https://thesugarscience.org

Interactive digital platform helping scientists who study type 1 diabetes connect, collaborate, and gain funding for their best ideas. All volunteer team has received much positive support from the global population of scientists studying type 1 diabetes, as well as from Beyond Type 1, JDRF, and IPITA. Provides curated conversations, events and technology to scientific T1D focused audience. Non profit entity funded by donations and sponsorships with industry and academic partners to provide unique collaborative benefits and programs to researchers in the T1D academic research community.

Proper citation: thesugarscience (RRID:SCR_020250) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/ze5-cell-analyzer?ID=OC62Q015

BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals.

Proper citation: Bio-Rad: ZE5 Cell Analyzer (RRID:SCR_019712) Copy   

•   Source: SciCrunch Registry

https://www.scionics.com/pyrat_de.html

Software tool for management of animal facility data by Scionics Computer Innovation GmbH. Used by laboratory animal facilities. Used by researchers, animal house managers, animal keepers and others to access their data from same source. Available in English, French, German, Italian, Portuguese and Spanish.

Proper citation: Python based Relational Animal Tracking (RRID:SCR_021014) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.7910/DVN/XD1A6B

Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups.

Proper citation: PROMIS 2 MY Health (RRID:SCR_021215) Copy   

•   Source: SciCrunch Registry

https://github.com/HeardLibrary/linked-data/tree/master/vanderbot

Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data.

Proper citation: VanderBot (RRID:SCR_021298) Copy   

•   Source: SciCrunch Registry

https://emea.support.illumina.com/sequencing/sequencing_software/experiment_manager/downloads.html

Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and NovaSeq 6000 Systems.

Proper citation: Illumina Experiment Manager (RRID:SCR_021202) Copy   

•   Source: SciCrunch Registry

https://gradepro.org/

Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.

Proper citation: GRADEpro (RRID:SCR_021308) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ichorCNA

Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample.

Proper citation: ichorCNA (RRID:SCR_024768) Copy   

•   Source: SciCrunch Registry

https://github.com/PaulingLiu/scibet

Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.

Proper citation: SciBet (RRID:SCR_024743) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfodlsu/rice-pilaf

Web app for post-GWAS/QTL analysis that performs slew of novel bioinformatics analyses to cross GWAS/QTL mapping results with host of publicly available rice databases.

Proper citation: RicePilaf (RRID:SCR_024945) Copy   

•   Source: SciCrunch Registry

https://github.com/bpucker/NAVIP

Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences.

Proper citation: NAVIP (RRID:SCR_024838) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/ion/research/research-departments/clinical-and-movement-neurosciences/centres-and-projects/queen-4

Platform for archival digital glass slide collection containing digital whole slide images from Lewy body disorders: Parkinson’s Disease, Parkinson’s Disease with Dementia and Dementia with Lewy Bodies, and control cases.E stained post-mortem brain tissues from patients with neurodegenerative diseases and controls.

Proper citation: QSBB Digital Pathology Resource (RRID:SCR_025020) Copy   

•   Source: SciCrunch Registry

https://inrae.github.io/pgd-mmdt/

Web ecosystem for sharing metadata. Designed to annotate datasets by creating metadata file to attach to storage space. Allows users to add descriptive metadata to datasets produced within collective of research unit, platform, multi-partner project, etc. to fit to data management plan about data organization and documentation, data storage and frictionless metadata sharing.

Proper citation: Maggot (RRID:SCR_025261) Copy   

•   Source: SciCrunch Registry

https://github.com/PhysiMeSS/PhysiMeSS

PhysiCell add-on which allows users to simulate ECM components as agents. PhysiCell addon for extracellular matrix modelling.

Proper citation: PhysiMeSS (RRID:SCR_025455) Copy   

•   Source: SciCrunch Registry

http://www.ucdavis.edu/

Proper citation: University of California at Davis; California; USA (RRID:SCR_012713) Copy   

•   Source: SciCrunch Registry

https://medicine.iu.edu/pharmacology-toxicology

Mission of Department of Pharmacology and Toxicology is to perform research to advance understanding of interactions of chemicals and drugs with living systems and to assist in development of new therapeutics and strategies to treat disease.

Proper citation: Indiana University School of Medicine Department of Pharmacology and Toxicology (RRID:SCR_006501) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/tools/gwama

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.

Proper citation: GWAMA (RRID:SCR_006624) Copy   

•   Source: SciCrunch Registry