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https://www.bioinformatics.nl/cgi-bin/emboss/getorf

Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences.

Proper citation: getorf (RRID:SCR_024691) Copy   

•   Source: SciCrunch Registry

https://www.noldus.com/erasmusladder

System consists of hardware and software for assessment of motor performance and motor learning in mice. Hardware includes two goal boxes with horizontal ladder in between. Touch sensitive rungs of the ladder make it possible to measure step durations and step types. ErasmusLadder software controls experiments by sending protocol and start command to apparatus. Sessions are performed automatically, and afterwards, data is sent back to software for storage and analysis.

Proper citation: Noldus: Erasmus Ladder (RRID:SCR_024695) Copy   

•   Source: SciCrunch Registry

https://focinator.com/

Open source software tool providing automated analysis of foci images including foci counting and colocalization of foci. Focinator v2-0 is able to perform multi channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of specific cell cycle phase.

Proper citation: Focinator (RRID:SCR_024697) Copy   

•   Source: SciCrunch Registry

http://opensciencesummit.com/

The objectives of Open Science Summit are to create an annual flagship event and news hub to build and maintain the identity of the international Open Science Movement as well as organize the various sub-communities into an effective, global, socio-technological force for rapid change in science/innovation policy. The Open Science Summit is the first and only event examining the full spectrum of the most crucial policy questions affecting the future of science. We consider the disruptive changes required to improve the functioning of 21st science, including institutional changes, new infrastructure for data driven science, and new practices. Scientists, Hackers, Students, Patients, and Activists, Entrepreneurs, Funders, Citizens should attend. Anyone who cares passionately about unleashing the full potential of Open Science to solve the big problems confronting humanity. Topics include: Synthetic Biology, Open Data, Open Access, Microfinance for Science, Citizen science, DIY Biology, Alternative Funding for Research, Open Source Drug Discovery, The Future of Patents, Accelerating Innovation, Open Genomics/Medicine, and More!

Proper citation: Open Science Summit (RRID:SCR_008006) Copy   

•   Source: SciCrunch Registry

http://www.globaleventslist.elsevier.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March, 4, 2021. A meeting resource which lists current and up-coming scientific and medical events by discipline, location, and date.

Proper citation: GlobalEventList (RRID:SCR_013960) Copy   

•   Source: SciCrunch Registry

http://brainhack.org/

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   

•   Source: SciCrunch Registry

http://ase.tufts.edu/terc/

Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease.

Proper citation: Tissue Engineering Resource Center (RRID:SCR_000103) Copy   

•   Source: SciCrunch Registry

http://www.ors.od.nih.gov/

The Office of Research Services (ORS) provides support to the NIH research mission by planning, directing and delivering scientific and regulatory activities, public safety, security, and services for the NIH community.

Proper citation: NIH Office of Research Services (RRID:SCR_000987) Copy   

•   Source: SciCrunch Registry

https://franklin.genoox.com/clinical-db/home

Connectivity hub across medical genetics domain. Network of genomic information. Supports all vendors and workflows and thus enables any genetic professional to deliver more accurate, more actionable data insights.

Proper citation: Franklin (RRID:SCR_024670) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells

MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.

Proper citation: MapMyCells (RRID:SCR_024672) Copy   

•   Source: SciCrunch Registry

https://docplayer.net/37250096-Fei-philips-cm120-tem.html

Transmission electron microscope with maximum acceleration voltage of 120 kv.Microscope primarily used for sample screening.

Proper citation: Philips: FEI CM120 BioTwin Transmission Electron Microscope (RRID:SCR_024709) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://datascience.uth.edu/medcis

NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research.

Proper citation: University of Texas Health Science at Houston Center for SUDEP Research (RRID:SCR_024700) Copy   

•   Source: SciCrunch Registry

https://www.infors-ht.com/en/shakers/incubator-shakers/multitron-standard/

Shaker for cultivation of microorganisms and cell cultures provides homogeneous conditions for cultivation up to 63 liters or 23 000 batches in parallel in less than square meter of space.

Proper citation: Multitron: Incubation Shaker (RRID:SCR_024668) Copy   

•   Source: SciCrunch Registry

http://www.projecthalo.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.

Proper citation: Project Halo (RRID:SCR_000136) Copy   

•   Source: SciCrunch Registry

https://covid-19.ensembl.org/

Ensembl SARS-Cov2 data portal.

Proper citation: Ensembl Covid-19 (RRID:SCR_024704) Copy   

•   Source: SciCrunch Registry

https://github.com/cchandre/Polarimetry

Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples.

Proper citation: PyPOLAR (RRID:SCR_024681) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

https://github.com/katiasmirn/PERFect#perfect-permutation-filtering-package-in-r

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Proper citation: PERFect (RRID:SCR_024682) Copy   

•   Source: SciCrunch Registry

http://rosalind.info/

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   

•   Source: SciCrunch Registry