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https://simtk.org/home/isim_interface

A simple Java graphical user interface for running the program ISIM. ISIM is a package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD but is no longer available. The version of ISIM used is available in the ISIM project on simtk.org.

Proper citation: Ion Simulator Interface (RRID:SCR_008267) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-16/search?q=%2A&l=&facet[]=Database:ResearchCrossroads

THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb. 05, 2014, however, NIF holds the Research Crossroads data and makes it available through Integrated Grants. World of publicly funded research aggregated into a database providing funding, publication, clinical trial and grant data from government and private research agencies. Advanced reporting and analysis tools are then used to connect research to researchers, organizations and topic areas to uncover non-obvious associations. Use ResearchCrossroads for: Researchers * Make your research visible to funding organizations and collaborators. * Connect with peers to stay up to date on their research progress * Update your investigator profile, biography and publications so funding organizations can find you * Discover available funding from private foundations and government funding organizations * Annotate your previous research grants with outcomes * Create a research diary and participate in discussions with your peers Foundations Participating in ResearchCrossroads is free if you share your research data. Send us a spreadsheet with your grant and investigator information. * Create a community for your researchers to learn from each other * Locate potential investigators and collaborators * Post available funding and be matched with investigator profiles * Access to analytical reporting of funding and research statistics * Update your personalized organization profile page * Display your logo in search results * Link to your ResearchCrossroads grants and investigator profiles from your own website Corporations, Academia & Governments Contact us about subscriptions to funding trend analytics and marketing opportunities. * In-depth reporting of 15 years of funding data from government and private institutions * Subscriptions available to advanced analysis & reporting tools * Display your corporate logo in search results * Update your organization profile page * Highly targeted marketing & advertising by research areas, keywords and categories of investigator * Register for notifications of the newest grants in your area of interest

Proper citation: ResearchCrossroads (RRID:SCR_008261) Copy   

•   Source: SciCrunch Registry

http://herpnet.org/

HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data. Sixty-four institutions are participating in the HerpNET community, with an open ended invitation to institutions who would like to join. Currently 56 institutions are available on the specimen searching portal, with data from over 5.5 million specimens available for searching. VertNet: The Future HerpNET, ORNIS, MaNIS and FishNet2 are taxon-based web portals that now serve georeferenced data on vertebrates from over 90 global institutions. Together these comprise VertNET, a cooperative project working to maintain and expand these distributed database projects. Future plans include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. Sponsors: This resource is supported by the National Science Foundation (NSF No. 0132303) and by a GBIF DIGIT .

Proper citation: HerpNET (RRID:SCR_008374) Copy   

•   Source: SciCrunch Registry

http://www.oege.org/software/hwe-mr-calc.shtml

This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation.

Proper citation: Hardy-Weinberg Equilibrium Calculator (RRID:SCR_008371) Copy   

•   Source: SciCrunch Registry

http://www.ieee.org/portal/site/iportals?WT.mc_id=hplogo_upleft

IEEE is the worlds largest professional association advancing innovation and technological excellence for the benefit of humanity. IEEE and its members inspire a global community to innovate for a better tomorrow through its highly cited publications, conferences, technology standards, and professional and educational activities. IEEE is the trusted voice for engineering, computing and technology information around the globe. Through its global membership, IEEE is a leading authority on areas ranging from aerospace systems, computers and telecommunications to biomedical engineering, electric power and consumer electronics among others. Members rely on IEEE as a source of technical and professional information, resources and services. To foster an interest in the engineering profession, IEEE also serves student members in colleges and universities around the world. Other important constituencies include prospective members and organizations that purchase IEEE products and participate in conferences or other IEEE programs. IEEE has: -more than 375,000 members in more than 160 countries; 45 percent of whom are from outside the United States -more than 80,000 student members -329 sections in ten geographic regions worldwide -1,860 chapters that unite local members with similar technical interests -1,789 student branches in 80 countries -483 student branch chapters at colleges and universities -390 affinity groups -- IEEE Affinity Groups are non-technical sub-units of one or more Sections or a Council. The Affinity Group patent entities are Consultants'' Network, Graduates of the Last Decade (GOLD), Women in Engineering (WIE) and Life Members (LM) IEEE''s core purpose is to foster technological innovation and excellence for the benefit of humanity. It will be essential to the global technical community and to technical professionals everywhere, and be universally recognized for the contributions of technology and of technical professionals in improving global conditions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IEEE (RRID:SCR_008314) Copy   

•   Source: SciCrunch Registry

http://www.accelrys.com/products/downloads/ds_visualizer/

A life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. Discovery Studio ADME Descriptors allow scientists to eliminate compounds with unfavorable ADME characteristics early in the discovery process and evaluate proposed structural refinements prior to synthesis. Applications of predictive ADME include pharmaceutical, cosmeceutical, and environmental sciences.

Proper citation: Discovery Studio Visualizer (RRID:SCR_008398) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time.

Proper citation: DelPhi (RRID:SCR_008669) Copy   

•   Source: SciCrunch Registry

http://www.sciencebuddies.org

Many science fairs have a group of people called a Scientific Review Committee (or SRC) that reviews each project application to ensure that all safety and legal requirements will be met and that the appropriate forms have been completed. The committee also reviews the completed project displays. Typically, a Scientific Review Committee is composed of at least three people: a biomedical scientist, a physical scientist, and a science teacher. Some fairs also have an Institutional Review Board (IRB), which reviews all proposed projects that in any way involve human beings. An IRB''s purpose is to ensure that the project will not present undue risk to the subjects.

Proper citation: Scientific Review Committee (RRID:SCR_008652) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nitrc

NITRC-wide community facilities: Forums, Wiki, Tracker, and News.

Proper citation: NITRC Community (RRID:SCR_009631) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Generic_Exome_Analysis_Plan

Outline of a generic plan for analysis of a whole exome sequencing project.

Proper citation: Generic Exome Analysis Plan (RRID:SCR_009656) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/incf_nidstf/

Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications.

Proper citation: INCF Neuroimaging Data Sharing (RRID:SCR_009497) Copy   

•   Source: SciCrunch Registry

http://psidev.sourceforge.net/mi/xml/doc/user/index.html

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. As a first step, the PSI is developing standards for two key areas of proteomics: mass spectrometry and protein-protein interaction data. The document describes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. Level 1 will describe protein interactions at a basic level that covers a large amount of currently available data. Subsequent levels will add capability to represent new molecular interaction information that the community wishes to exchange. The scope of PSI MI is currently limited to protein-protein interactions. Other molecules, such as small molecules, DNA and RNA maybe taken into account in the future. The PSI MI format is a data exchange format for protein-protein interactions. It is not a proposed database structure. The purpose of the document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. PSI MI was designed by a group of people including representatives from database providers and users in both academia and industry. PSI MI is supported by the DIP, MINT, IntAct, BIND and HPRD databases.

Proper citation: PSI-MI (RRID:SCR_010710) Copy   

•   Source: SciCrunch Registry

http://scienceexchange.com/

Access service resource which connects labs needing and offering experimental services. Users can search for academic and government labs and experimental services, request and compare service quotes, and directly communicate with labs to arrange orders.

Proper citation: ScienceExchange (RRID:SCR_010620) Copy   

•   Source: SciCrunch Registry

http://purl.org/

Web addresses that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources, PURLs provide a level of indirection that allows the underlying Web addresses of resources to change over time without negatively affecting systems that depend on them. This capability provides continuity of references to network resources that may migrate from machine to machine for business, social or technical reasons.

Proper citation: Purl (RRID:SCR_010238) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/microbe-inotech-laboratories-inc

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22,2024. Microbe Inotech Laboratories, Inc. (The MiL, Inc.) is your direct source for answers to all of your microbiological inquiries. We are a full-service laboratory that can provide microbial and biochemical analyses for your specific industry. Whether you are concerned about food safety or you need microbiological testing for your field, Microbe Inotech Laboratories has the expertise and advanced technologies to provide solid answers. We have more than 18 years of experience in helping our customers find practical solutions to their microbiological needs. We offer our broad range of services to manufacturers, retailers, processors, and many other industries. Our laboratory divisions are environmental, food safety, industrial, pharmaceutical and governmental.

Proper citation: Microbe Inotech Laboratories Inc. (RRID:SCR_012215) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/parabase-genomics

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2, 2024. Parabase Genomics is a molecular diagnostic company offering whole exome sequencing services to physicians and researchers with a specialty in the identification of rare variants associated with Mendelian Disorders. Our sample processing and variant analysis pipelines are highly optimized for calling rare variants that are normally missed by less optimized workflows. At Parabase Genomics, we have combined a team of innovators and experts in genomics, pediatrics and targeted sequencing that are not available at other service organizations. Our team is also unique in that we can deliver both research and well as CLIA/CAP certified exomes with insurance reimbursement.

Proper citation: Parabase Genomics (RRID:SCR_012336) Copy   

•   Source: SciCrunch Registry

https://www.genome-cloud.com/user/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29, 2019. A cloud platform for next-generation sequencing analysis and storage. Services include: * g-Analysis: Automated genome analysis pipelines at your fingertips * g-Cluster: Easy-of-use and cost-effective genome research infrastructure * g-Storage: A simple way to store, share and protect data * g-Insight: Accurate analysis and interpretation of biological meaning of genome data

Proper citation: GenomeCloud (RRID:SCR_011886) Copy   

•   Source: SciCrunch Registry

https://ocimumbio.com/

Comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress, ToxExpress) and Bio-IT consulting services.

Proper citation: Ocimum Biosolutions (RRID:SCR_012307) Copy   

•   Source: SciCrunch Registry

http://www.ngsleaders.org/

A community created to advance the use and value of next-generation sequencing through knowledge sharing.

Proper citation: NGS Leaders (RRID:SCR_011982) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/microbiology-quality-associates-inc

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 22, 2024. Microbiology & Quality Associates, Inc., located in the San Francisco Bay Area, is a service organization providing a variety of services to life sciences companies. Our services include: contract biotech development services, testing services, consulting, validation services, calibration services, training, and scientific resources. MQA is FDA registered. Our Quality System comply with GXP regulations and ISO 17025/9001. We provide services to a wide variety of companies in biotechnology, pharmaceutical, medical devices, nutritional products, dialysis centers, semiconductors, and other industries. MQA staff has many years of hands-on experience at pharmaceutical, biotechnology and medical device companies.

Proper citation: Microbiology and Quality Associates (RRID:SCR_012270) Copy   

•   Source: SciCrunch Registry