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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://www.electrontomography.org/?page_id=446
Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler.
Proper citation: Protomo (RRID:SCR_017296) Copy
http://idr.openmicroscopy.org/about/
Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology.
Proper citation: Image Data Resource (IDR) (RRID:SCR_017421) Copy
Medical image repository to store medical research data.
Proper citation: SICAS Medical Image Repository (RRID:SCR_017420) Copy
https://beast.community/tempest
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Proper citation: TempEst (RRID:SCR_017304) Copy
https://github.com/drchrisch/SynapseLocator
Software tool that combines steps of image processing, non rigid image registration, and spot localisation. Performs registration of 3D imaging data and localization of spots, active synapses in light microscopy images, in semi automatic mode with graphical user interface.
Proper citation: SynapseLocator (RRID:SCR_017263) Copy
https://epigenie.com/epigenetic-tools-and-databases/
Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team.
Proper citation: Epigenie (RRID:SCR_017494) Copy
https://www.adobe.com/lightroom
Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device.
Proper citation: Adobe Photoshop Lightroom (RRID:SCR_018012) Copy
https://github.com/LaBiOS/Transcriptive
Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results.
Proper citation: Transcriptive (RRID:SCR_017545) Copy
Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
Proper citation: MOON (RRID:SCR_018005) Copy
Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way.
Proper citation: brainhack.org (RRID:SCR_000195) Copy
http://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU
Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.
Proper citation: MUMmerGPU (RRID:SCR_001200) Copy
Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.
Proper citation: Karmanos Cancer Institute (RRID:SCR_000508) Copy
http://www.bioinformatics.org/wiki/BioWiki
A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.
Proper citation: BioWiki (RRID:SCR_000629) Copy
A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.
Proper citation: IFTI-Mirage (RRID:SCR_000505) Copy
http://www.atsdr.cdc.gov/toxprofiles
A database of information about contaminants found at hazardous waste sites. The toxicological profiles are cataloged by chemical with the NTIS order number.
Proper citation: CDC Toxprofiles (RRID:SCR_000900) Copy
http://dunham.gs.washington.edu/protocols.shtml
A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.
Proper citation: Maitreya Dunham's Lab (RRID:SCR_000784) Copy
http://www.nitrc.org/projects/nihgrantees/
This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration.
Proper citation: Grantees Meeting for NITRC (RRID:SCR_000419) Copy
http://jsp.weigelworld.org/expviz/expviz.jsp
A visualization tool with microarray data and sample descriptions from the AtGenExpress project, which contains Affymetrix microarray data for Arabidopsis, a small flowering plant related to mustard and cabbage. This plant is used as a model organism in plant biology.
Proper citation: AtGenExpess - Weigel World (RRID:SCR_000777) Copy
A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.
Proper citation: Rosalind (RRID:SCR_006233) Copy
Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.
Proper citation: Drug Design Data Resource (RRID:SCR_000497) Copy
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