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http://research.cs.wisc.edu/wham/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output

Proper citation: WHAM (RRID:SCR_005497) Copy   

•   Source: SciCrunch Registry

http://www.nescent.org/

The National Evolutionary Synthesis Center (NESCent) is a nonprofit science center dedicated to cross-disciplinary research in evolution. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries. Synthetic research in evolutionary science takes many forms but includes integrating novel data sets and models to address important problems within a discipline, developing new analytical approaches and tools, and combining methods and perspectives from multiple disciplines to answer and even create new fundamental scientific questions. NESCent facilitates such synthetic research by providing an environment for fertile interactions among scientists. Our Science and Synthesis program sponsors postdoctoral fellows and sabbatical scholars as resident scientists, and two kinds of meetings, working groups and catalysis meetings. Catalysis meetings provide a novel mechanism for bringing together diverse research communities and cultures to identify common interests, while working groups provide an opportunity for scientists to work together intensively on fundamental synthetic questions over a several-year period. These activities are community driven through our application process and evaluated by an external advisory board. Our Informatics program provides state of the art informatics tools to visiting and in-house scientists and aims to take the lead in assembling novel databases and developing new analytical tools for evolutionary biology. Finally it is sponsoring a major initiative to provide a digital data repository for work in evolutionary biology. NESCent''s Education and Outreach group communicates the results of evolutionary biology research to the general public and scientific community, provides outreach to groups who are underrepresented in evolutionary biology and works to improve evolution education.

Proper citation: NESCent - National Evolutionary Synthesis Center (RRID:SCR_005911) Copy   

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http://rankprop.gs.washington.edu/svm-fold/

This web server makes predictions of family, superfamily and fold level classifications of proteins based on the Structural Classification of Proteins (SCOP) hierarchy using the Support Vector Machine (SVM) learning algorithm. SVM-FOLD detects subtle protein sequence similarities by learning from all available annotated proteins, as well as utilizing potential hits as identified by PSI-BLAST. Predictions of classes of proteins that do not have any known example with a significant pairwise PSI-BLAST E-value can still be found using SVMs.

Proper citation: SVM-fold: Protein Fold Prediction (RRID:SCR_006834) Copy   

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http://www.softpedia.com/get/Science-CAD/DynGO.shtml

DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible

Proper citation: DynGO (RRID:SCR_007009) Copy   

•   Source: SciCrunch Registry

http://lamp.icsi.berkeley.edu/lamp/

A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.

Proper citation: Local Ancestry in adMixed Populations (RRID:SCR_001258) Copy   

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http://arf.fsu.edu/

National repository for geological materials collected in polar regions housing over 20,000 meters of deep-sea core sediment and over 5,000 kg of dredge, trawl, and grab samples, the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises. The Facility also houses and curates nearly 3,000 meters of rotary cored geological material acquired by NSF supported drilling programs in the Antarctic. Replacement cost of this core inventory in terms of ship and ice-based drilling is conservatively estimated to be in the range of $150 to $200M. SESAR or the the System for Earth Sample Registration is a service provided by the IDEA. SESAR operates the registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search. Facility services include:
* curation of the existing collections at the facility
* onsite ship and land based curatorial services
* receipt and processing of new cores
* core description and publication of core descriptions
* distribution of samples from the collection to authorized scientists
* hosting of scientific meetings and workshops
* tours, lectures, and student education and training in Antarctic geoscience
* maintenance of:
** a core and sample database
** an Antarctic geology and marine geology reference library and a searchable End Note computer database of the entire collection
** a satellite IODP/MRC for nannofossils and diatoms

Proper citation: Antarctic Marine Geology Research Facility (RRID:SCR_002213) Copy   

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http://bgsc.org/

Supplier of genetically characterized strains, cloning vectors, and bacteriophages for the genus Bacillus and related organisms. The BGSC can distribute these materials to qualified scientists and educators throughout the world.

Proper citation: Bacillus Genetic Stock Center (BGSC) (RRID:SCR_014950) Copy   

•   Source: SciCrunch Registry

https://rmats.sourceforge.io

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: rMATS (RRID:SCR_023485) Copy   

•   Source: SciCrunch Registry

https://github.com/wlloyduw/ContainerProfiler

Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers.

Proper citation: ContainerProfiler (RRID:SCR_023770) Copy   

•   Source: SciCrunch Registry

https://gateway-nmr.osu.edu/capablities#:~:text=Bruker%20Avance%20Neo%201.2%20GHz%20NMR%20Spectrometer

Spectrometer represents the pinnacle of commercial nuclear magnetic resonance technology. Operating at 28.2 Tesla, this ultra-high-field system is primarily used for advanced structural biology, pharmaceutical research, and materials science. Delivers the highest commercially available spectral resolution, crucial for investigating complex protein dynamics, functional molecular disorders, and viral structures. Console:Avance Neo; Magnet:Gateway; Field Strength: 1.2 GHz; Software:TopSpin 4.4.1 on CentOS 7; Probes:3mm TCI cryoprobe; 3mm BBI room-temperature; 3.2mm HX low-gamma MAS; 1.9mm HX high-gamma MAS; 1.3mm HCN fast MAS; 0.7mm HCN ultra-fast MAS; Chilled SampleCase (up to 24 samples); Automated Tuning and Matching (ATM); Nitrogen Liquefier.

Proper citation: Bruker: Avance Neo 1.2 GHz NMR Spectrometer (RRID:SCR_028512) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/metagear/index.html

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) Copy   

•   Source: SciCrunch Registry

https://github.com/dereneaton/ipyrad

Software interactive toolkit for assembly and analysis of restriction site associated genomic data sets including RAD, ddRAD, GBS, for population genetic and phylogenetic studies. Used for interactive assembly and analysis of RADseq data sets.

Proper citation: ipyrad (RRID:SCR_022016) Copy   

•   Source: SciCrunch Registry

https://github.com/mhammell-laboratory/TEtranscripts

Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool.

Proper citation: TEtranscripts (RRID:SCR_023208) Copy   

•   Source: SciCrunch Registry

https://benjjneb.github.io/dada2/

Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.

Proper citation: DADA2 (RRID:SCR_023519) Copy   

•   Source: SciCrunch Registry

http://anya.igsb.anl.gov/Geneways/GeneWays.html

System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

Proper citation: GeneWays (RRID:SCR_000572) Copy   

•   Source: SciCrunch Registry

http://www.fgsc.net/

The Fungal Genetics Stock Center is a resource available to the Fungal Genetics research community and to educational and research organizations in general. While some fungi can cause disease in humans, most people have innate immunity against fungi. Some people with diseases of the immune system are at increased risk of infection by fungi. Drugs have been developed in the last 5 years that help with this. Fungal Genetics is the study of genes and genetic traits in fungi. In the past this has been important in the elucidation of what a gene is, what the genetic material is, how genes relate to enzymes, how enzymes relate to traits and how important traits change or evolve. In the present, Fungal Genetics is important to understanding how fungi are pathogens of plants and animals, how fungi can be used in industry for the production of enzymes, chemicals, food, and drugs. Fungi are also essential to processing bio-mass in the attempt to use ethanol as a fuel source. The FGSC is funded largely by a grant from the National Science Foundation (Award Number 0235887) of the United States of America. Sponsors: Supported by a grant from the National Science Foundation.

Proper citation: Fungal Genetics Stock Center (RRID:SCR_008143) Copy   

•   Source: SciCrunch Registry

https://elegansvariation.org/

Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.

Proper citation: Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) Copy   

•   Source: SciCrunch Registry

http://www.chlamycollection.org/

Central repository that receives, catalogs, preserves, and distributes wild type and mutant cultures of the green alga Chlamydomonas reinhardtii, as well as useful molecular reagents and kits for education and research.

Proper citation: Chlamydomonas Resource Center (RRID:SCR_014960) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/resources/

Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J

Proper citation: Genes to Cognition - Biological Resources (RRID:SCR_001675) Copy   

•   Source: SciCrunch Registry

http://biodev.ece.ucsb.edu/projects/bisquik/wiki

A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bisque (RRID:SCR_005564) Copy   

•   Source: SciCrunch Registry