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http://www.microbeworld.org/index.php?option=com_content&view=category&layout=blog&id=99&Itemid=259

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Parasitism (TWiP) is a podcast about eukaryotic parasites hosted by Vincent Racaniello and Dick Despommier. Following in the path of their successful podcast ''This Week in Virology'' (TWiV), they strive for an informal yet informative conversation about parasites which is accessible to everyone, no matter what their science background. As science Professors at Columbia University, they have spent their entire academic careers directing research laboratories focused on parasites (Dick) and viruses (Vincent). Their enthusiasm for teaching inspired them to reach beyond the classroom with new media. TWiP is for everyone who wants to learn about parasites in a relaxing way. Music used on TWiP is composed and performed by Ronald Jenkees and used with permission.

Proper citation: TWiP - This Week in Parasitism (RRID:SCR_006788) Copy   

•   Source: SciCrunch Registry

http://grants.nih.gov/grants/oer.htm

OER serves as a vital interface between the NIH and the biomedical research community by guiding investigators through the process of attaining grants funding and helping them understand and navigate through federal policies and procedures. OER supports extramural research by providing policy and guidance to the 24 NIH Institutes and Centers that award grants. Extramural grants account for approximately 84 percent of NIH''s 29 billion budget. These are awarded to investigators throughout the U.S. and abroad. Approximately 10 percent of the NIH budget supports NIH intramural investigators, NIH staff who conduct research.

Proper citation: Office of Extramural Research NIH (RRID:SCR_006547) Copy   

•   Source: SciCrunch Registry

http://ajp.psychiatryonline.org/audio.aspx

An audio summary of highlights and key articles from each issue of The American Journal of Psychiatry. Users may subscribe to the podcast to get automatic updates with each issue or download each issue''s audio file individually.

Proper citation: American Journal of Psychiatry Podcasts (RRID:SCR_007070) 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

https://github.com/gobics/cocopye

Software tool for quality assessment of microbial genomes. Used to predict completeness and contamination of bacterial and archaeal genomes. Provides taxonomic classification of the input. Feature-based learning and prediction of genome quality indices.

Proper citation: CoCoPyE (RRID:SCR_025756) Copy   

•   Source: SciCrunch Registry

https://mouseinfo.kr/

Center to develop genetically engineered mice, analyze mouse phenotypes, and establish nationwide infrastructure for mouse research. South Korean government designated KMPC as principal organization for preclinical trials using mice and hamsters.

Proper citation: Korea Mouse Phenotyping Center (RRID:SCR_026052) Copy   

•   Source: SciCrunch Registry

http://firebrowse.org/

Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models.

Proper citation: FireBrowse (RRID:SCR_026320) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebWarp

Web application for nonlinear refinement of image registration after WebAlign.

Proper citation: WebWarp (RRID:SCR_026759) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebAlign

Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).

Proper citation: WebAlign (RRID:SCR_026758) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/BIGapp

Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS).

Proper citation: BIGapp (RRID:SCR_026676) Copy   

•   Source: SciCrunch Registry

https://github.com/ngyuilun/EC-LMGraph

Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction.

Proper citation: EC-LMGraph (RRID:SCR_027317) Copy   

•   Source: SciCrunch Registry

https://www.mcw.edu/departments/pathology-and-laboratory-medicine/research/mcw-tissue-bank

College of American Pathologists-accredited biorepository that collects, processes, securely stores, and distributes human biospecimens (tissues and blood products) for medical research. Tissue Bank that is a CAP-accredited biorepository supporting four human consent programs. Provides fresh and frozen tissue and biological materials with known preanalytical variables to researchers as well as provides specialized processing and imaging services.

Proper citation: Medical College of Wisconsin Tissue Bank (RRID:SCR_027842) Copy   

•   Source: SciCrunch Registry

https://github.com/mzlab-research/SMIntegration

Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.

Proper citation: SMIntegration (RRID:SCR_027925) Copy   

•   Source: SciCrunch Registry

http://www.laureateinstitute.org/

Clinical neuroscience research institute in Tulsa, Oklahoma, dedicated to identifying biological markers and developing advanced interventions for mental health conditions, including disorders of mood, anxiety, eating, and substance use.

Proper citation: Laureate Institute for Brain Research; Oklahoma; USA (RRID:SCR_028639) Copy   

•   Source: SciCrunch Registry