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https://rockd.org/

Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.

Proper citation: rockd (RRID:SCR_024431) Copy   

•   Source: SciCrunch Registry

https://www.planetmicrobe.org/

Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data.

Proper citation: Planet Microbe (RRID:SCR_024478) 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://www.agic.umn.edu/

Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.

Proper citation: Polar Geospatial Center (RRID:SCR_000402) Copy   

•   Source: SciCrunch Registry

https://github.com/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry

http://lepr.ofm-research.org/

Database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems.

Proper citation: Library of Experimental Phase Relations (RRID:SCR_002202) Copy   

•   Source: SciCrunch Registry

https://enigma.lbl.gov/regprecise/

Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RegPrecise (RRID:SCR_002149) Copy   

•   Source: SciCrunch Registry

http://www.earthchem.org/seddb

Geochemical database for marine and terrestrial sediments primarily from the published literature containing a full range of analytical values for sediment samples, primarily from marine sediment cores. It includes major and trace element concentrations, radiogenic and stable isotope ratios, and data for a plethora of materials such as organic and inorganic components, leachates, and size fractions. SedDB also archives a vast array of metadata relating to the individual sample.

Proper citation: SedDB (RRID:SCR_002210) Copy   

•   Source: SciCrunch Registry

http://www.earthchem.org/petdb

Accepts and provides access to geochemical and petrological data for ocean floor igneous and metamorphic rocks, (whole rock, volcanic, glass, mineral, and melt inclusion analyses), and mantle and lower-crustal xenolith samples. Data are compiled primarily from the published literature. Authors are encouraged to submit their datasets and databases to EarthChem.

Proper citation: PetDB (RRID:SCR_002209) Copy   

•   Source: SciCrunch Registry

http://gocognitive.net/

Free access to materials for students, educators, and researchers in cognitive psychology and cognitive neuroscience. Currently there are about a dozen demonstrations and more than 30 videos that were produced over the last two years. The basic philosophy of goCognitive rests on the assumption that easy and free access to high-quality content will improve the learning experience of students and will enable more students to enjoy the field of cognitive psychology and cognitive neuroscience. There are a few parts of goCognitive that are only available to registered users who have provided their email address, but all of the online demonstrations and videos are accessible to the everyone. Both new demonstrations and new video interviews will continually be added to the site. Manuals for each of the demonstration are being created and available as pdf files for download. Most of the demonstrations are pretty straightforward - but in some cases, especially if you would like to collect data - it might be a good idea to look over the manual. There are different ways in which you can get involved and contribute to the site. Your involvement can range from sending us feedback about the demonstrations and videos, suggestions for new materials, or the simple submission of corrections, to the creation or publication of demonstrations and videos that meet our criteria. Down the road we will make the submission process easier, but for now please contact swerner (at) uidaho dot edu for more information. NSF student grant Undergraduate students can apply through goCognitive for an $1,100 grant to co-produce a new video interview with a leading researcher in the field of cognitive neuroscience. The funding has been provided by the National Science Foundation.

Proper citation: goCognitive (RRID:SCR_006154) Copy   

•   Source: SciCrunch Registry

http://www.scrible.com/#desktop

We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar.

Proper citation: scrible (RRID:SCR_008882) Copy   

•   Source: SciCrunch Registry

http://www.cravat.us/

A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.

Proper citation: CRAVAT (RRID:SCR_012776) Copy   

•   Source: SciCrunch Registry

http://www.collectf.org/browse/home/

A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.

Proper citation: CollecTF (RRID:SCR_014405) Copy   

•   Source: SciCrunch Registry

http://msub.csbio.unc.edu/

A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.

Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

https://www.umass.edu/ials/pccl-database

Collection of plant species for use by both academia and industry.The PCCL enables R&D exploitation of monocot, dicot and gymnosperm cultures.

Proper citation: Plant Cell Culture Library (PCCL) (RRID:SCR_016784) Copy   

•   Source: SciCrunch Registry

http://www.ldeo.columbia.edu/core-repository

Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator.

Proper citation: Lamont-Doherty Core Repository (RRID:SCR_002216) Copy   

•   Source: SciCrunch Registry

http://lrc.geo.umn.edu/laccore/

Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs.

Proper citation: National Lacustrine Core Facility (RRID:SCR_002215) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/annotation/fungi/fgi/

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

Proper citation: Fungal Genome Initiative (RRID:SCR_003169) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry