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https://nanohub.org

A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content.

Proper citation: nanoHUB (RRID:SCR_013963) Copy   

•   Source: SciCrunch Registry

https://github.com/CBL-ORION/orion

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

•   Source: SciCrunch Registry

https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_retriever

Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly.

Proper citation: LTR_retriever (RRID:SCR_017623) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/vcu-nanomaterials-characterization-center-vcu

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Nanomaterials Characterization Center at Virginia Commonwealth University is a state of the art 4000 sq. ft. facility located within the new Health and Life Science Engineering Facility. The Center provides an academic structure for students in natural sciences, mathematics, engineering, and medicine to participate in nanoscience and nanotechnology research to acquire the skills necessary to pursue such careers. In the past year, VCU received two National Science Foundation major research instrumentation grants totaling more than $1.6 million to expand its capabilities for research in materials science. Combining these federal awards with state instrumentation grants and private donations, the facility has been able to build a state of the art facility with over $5 million in new equipment. This new equipment will allow faculty and student researchers from both VCU campuses, as well as other universities.

Proper citation: VCU Nanomaterials Characterization Center (RRID:SCR_012162) Copy   

•   Source: SciCrunch Registry

http://www.marine-geo.org/portals/antarctic/

Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.

Proper citation: Antarctic and Southern Ocean Data Portal (RRID:SCR_002193) Copy   

•   Source: SciCrunch Registry

http://psidonline.isr.umich.edu/

Long-term longitudinal dataset with information on generational links and socioeconomic and health conditions of individuals over time. The central foci of the data are economic and demographic, with substantial detail on income sources and amounts, wealth, savings, employment, pensions, family composition changes, childbirth and marriage histories, and residential location. Over the life of the PSID, the NIA has funded supplements on wealth, health, parental health and long term care, housing, and the financial impact of illness, thus also making it possible to model retirement and residential mobility. Starting in 1999, much greater detail on specific health conditions and health care expenses is included for respondent and spouse. Other enhancements have included a question series about emotional distress (2001); the two stem questions from the Composite International Diagnostic Interview to assess symptoms of major depression (2003); a supplement on philanthropic giving and volunteering (2001-03); a question series on Internet and computer use (2003); linkage to the National Death Index with cause of death information for more than 4,000 individuals through the 1997 wave, updated for each subsequent wave; social and family history variables and GIS-linked environmental data; basic data on pension plans; event history calendar methodology to facilitate recall of employment spells (2001). The reporting unit is the family: single person living alone or sharing a household with other non-relatives; group of people related by blood, marriage, or adoption; unmarried couple living together in what appears to be a fairly permanent arrangement. Interviews were conducted annually from 1968 through 1997; biennial interviewing began in 1999. There is an oversample of Blacks (30%). Waves 1990 through 1995 included a 20% Hispanic oversample; within the Hispanic oversample, Cubans and Puerto Ricans were oversampled relative to Mexicans. All data from 1994 through 2001 are available as public release files; prior waves can be obtained in archive versions. The special files with weights for families are also available. Restricted files include the Geocode Match File with information for 1968 through 2001, the 1968-2001 Death File, and the 1991 Medicare Claims File. * Dates of Study: 1968-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size: 65,000+ Links * ICPSR Series: http://www.icpsr.umich.edu/icpsrweb/ICPSR/series/00131 * ICPSR 1968-1999: Annual Core Data: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/07439 * ICPSR 1968-1999: Supplemental Files: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03202 * ICPSR 1989-1990: Latino Sample: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03203

Proper citation: Panel Study of Income Dynamics (RRID:SCR_008976) Copy   

•   Source: SciCrunch Registry

http://nis.princeton.edu/

Public use data set on new legal immigrants to the U.S. that can address scientific and policy questions about migration behavior and the impacts of migration. A survey pilot project, the NIS-P, was carried out in 1996 to inform the fielding and design of the full NIS. Baseline interviews were ultimately conducted with 1,127 adult immigrants. Sample members were interviewed at baseline, 6 months, and 12 months, with half of the sample also interviewed at three months. The first full cohort, NIS-2003, is based on a nationally representative sample of the electronic administrative records compiled for new immigrants by the US government. NIS-2003 sampled immigrants in the period May-November 2003. The geographic sampling design takes advantage of the natural clustering of immigrants. It includes all top 85 Metropolitan Statistical Areas (MSAs) and all top 38 counties, plus a random sample of other MSAs and counties. Interviews were conducted in respondents'' preferred languages. The baseline was multi-modal: 60% of adult interviews were administered by telephone; 40% were in-person. The baseline round was in the field from June 2003 to June 2004, and includes in the Adult Sample 8,573 respondents, 4,336 spouses, and 1,072 children aged 8-12. A follow-up was planned for 2007. Several modules of the NIS were designed to replicate sections of the continuing surveys of the US population that provide a natural comparison group. Questionnaire topics include Health (self-reports of conditions, symptoms, functional status, smoking and drinking history) and use/source/costs of health care services, depression, pain; background; (2) Background: Childhood history and living conditions, education, migration history, marital history, military history, fertility history, language skills, employment history in the US and foreign countries, social networks, religion; Family: Rosters of all children; for each, demographic attributes, education, current work status, migration, marital status and children; for some, summary indicators of childhood and current health, language ability; Economic: Sources and amounts of income, including wages, pensions, and government subsidies; type, value of assets and debts, financial assistance given/received to/from respondent from/to relatives, friends, employer, type of housing and ownership of consumable durables. * Dates of Study: 2003-2007 * Study Features: Longitudinal * Sample Size: 13,981

Proper citation: New Immigrant Survey (RRID:SCR_008973) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/icr

Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques.

Proper citation: National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility (RRID:SCR_017361) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/emr/

EMR Facility offers home-built, high-frequency and high-field continuous-wave instruments providing frequency coverage from 9 GHz to 1 THz, with additional frequencies available up to 2.5 THz using molecular gas laser. EMR covers variety of magnetic resonance techniques associated with electron like Electron Paramagnetic/Spin Resonance (EPR/ESR). EPR/ESR can be performed on any sample that has unpaired electron spins and used in applications in physics, materials science, chemistry and biology, including studies of impurity states, molecular clusters, antiferromagnetic, ferromagnetic and thin film compounds, natural or induced radicals, optically excited paramagnetic states, electron spin-based quantum information devices, transition-metal based catalysts; and for structural and dynamical studies of metallo-proteins, spin-labeled proteins and other complex bio-molecules and their synthetic models.

Proper citation: National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility (RRID:SCR_017359) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/dc-field

Facility located at MagLab headquarters near Florida State University in Tallahassee. Contains 14 resistive magnet cells connected to 56 megawatt DC power supply and 15,000 square feet of cooling equipment to remove heat generated by magnets. Includes several superconducting magnets operating at millikelvin temperatures. Among these instruments is 45-tesla hybrid magnet, which offers scientists strongest continuous magnetic field in world. Research is supported by magnet plant and cryogenic system operators. Technicians design, build and repair instruments for user research.

Proper citation: National High Magnetic Field Lab DC Field Core Facility (RRID:SCR_017358) Copy   

•   Source: SciCrunch Registry

https://sites.northwestern.edu/nucapt/

Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials.

Proper citation: Northwestern University Center for Atom Probe Tomography Core Facility (RRID:SCR_017770) Copy   

•   Source: SciCrunch Registry

http://www.columbia.edu/cu/biology/resources/proteomics/

Core provides identification of proteins and metabolites with differential quantitative expression in cells, tissues or in protein affinity purifications. Particular emphasis is on quantitative analysis of posttranslational modifications such as phosphorylation.

Proper citation: Columbia University Quantitative Proteomics and Metabolomics Core Facility (RRID:SCR_017747) Copy   

•   Source: SciCrunch Registry

http://sites.northwestern.edu/pldcore/

Core provides means to grow thin films of metals and metal oxides. Facility contains two state of art deposition chambers PVD PLD/MBE 2300 and a PVD nanoPLD 1000. PLD provides convenient way to make thin films of materials heretofore studied in bulk by pressing and sintering target from bulk material; facilities are available at Northwestern for pressing and sintering of targets.

Proper citation: Northwestern University Pulsed Laser Deposition Core Facility (RRID:SCR_017889) Copy   

•   Source: SciCrunch Registry

http://xray.facilities.northwestern.edu/

Core provides general purpose x-ray equipment for diffraction and fluorescence studies. Examples of current measurements are: powder diffraction, single-crystal diffraction, thin-film reflectivity, thin-film diffraction, crystal truncation rod scattering, small angle scattering, Laue diffraction, residual stress, pole figures, EDX-ray fluorescence, x-ray standing waves, high-resolution x-ray diffraction, and grazing incidence small angle scattering.

Proper citation: Northwestern University Jerome B. Cohen X-ray Diffraction Core Facility (RRID:SCR_017866) Copy   

•   Source: SciCrunch Registry

http://www.sb.fsu.edu/~rsref/Distribution/roadmap_distribution.htm

Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Roadmap (RRID:SCR_017207) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.princeton.edu/conservation/

Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.

Proper citation: Conservation (RRID:SCR_016064) Copy   

•   Source: SciCrunch Registry

https://www.ezbiocloud.net/tools/orthoaniu

Software tool for calculating average nucleotide identity.

Proper citation: OrthoANIu (RRID:SCR_022562) Copy   

•   Source: SciCrunch Registry

http://www.pyrosetta.org/

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

Proper citation: PyRosetta (RRID:SCR_018541) Copy   

•   Source: SciCrunch Registry

https://github.com/raphael-group/chisel

Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers.

Proper citation: CHISEL (RRID:SCR_023220) Copy   

•   Source: SciCrunch Registry