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https://github.com/NuttyLogic/EpigeneticPacemaker

Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest.

Proper citation: Epigenetic Pacemaker (RRID:SCR_018158) Copy   

•   Source: SciCrunch Registry

https://atagousa.corecommerce.com/PAL-10S-p358.html

Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml.

Proper citation: Atago: PAL-10S Pocket Refractometer (RRID:SCR_018439) Copy   

•   Source: SciCrunch Registry

https://github.com/vinguyenle/k-FLBPCM-method

Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.

Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy   

•   Source: SciCrunch Registry

https://github.com/yhoogstrate/dr-disco

Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.

Proper citation: Dr. Disco (RRID:SCR_021739) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

http://carbonyldb.missouri.edu/CarbonylDB/index.php/

Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.

Proper citation: CarbonylDB (RRID:SCR_023924) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhenjiangFan/DAG-deepVASE

Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.

Proper citation: DAG-deepVASE (RRID:SCR_023612) Copy   

•   Source: SciCrunch Registry

http://www.dbemt.bioinfo-minzhao.org/

Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.

Proper citation: dbEMT 2 (RRID:SCR_024692) Copy   

•   Source: SciCrunch Registry

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://corelifesciences.com

A commercial organization that supplies researchers with life science instruments, reagents and consumables, and lab services.

Proper citation: Core Life Sciences (RRID:SCR_000138) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/current-users/morphometry-birn/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains.

Proper citation: Morphometry BIRN (RRID:SCR_000155) Copy   

•   Source: SciCrunch Registry

http://www.hunter.cuny.edu/chemistry/facilities/nmr/home

A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages.

Proper citation: Hunter NMR Spectroscopy Facility (RRID:SCR_000883) Copy   

•   Source: SciCrunch Registry

http://www.cbrc.jp/htbin/show_tffactor_mw

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016.

A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese.

Proper citation: TFFACTOR (RRID:SCR_000519) Copy   

•   Source: SciCrunch Registry

http://www.hivebench.com/

A commercial software laboratory notebook.

Proper citation: hivebench (RRID:SCR_000915) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=13

Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Chromas (RRID:SCR_000598) Copy   

•   Source: SciCrunch Registry

http://famu.eagle-i.net/i/00000137-5195-0786-f0f1-ede280000000

A laboratory equipped with laser-based flow cytometric instruments, the main one being the Becton Dickinson two-laser FACScalibur analyzer. This facility provides a resource for analytical and preparative studies of cells using flow cytometry to the FAMU biomedical researchers. This facility offers FACS acquisition and analysis for detecting cell surface or intracellular proteins, measuring apoptosis, cell cycle, cellular physiology that have both biomedical and clinical applications.

Proper citation: FAMU Flow cytometry laboratory (RRID:SCR_000877) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-genvision.aspx

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

Proper citation: GenVision (RRID:SCR_001166) Copy   

•   Source: SciCrunch Registry

http://lehd.did.census.gov/led/

A dataset that combines federal and state administrative data on employers and employees with core Census Bureau censuses and surveys, while protecting the confidentiality of people and firms that provide the data. This data infrastructure facilitates longitudinal research applications in both the household / individual and firm / establishment dimensions. The specific research is targeted at filling an important gap in the available data on older workers by providing information on the demand side of the labor market. These datasets comprise Title 13 protected data from the Current Population Surveys, Surveys of Income and Program Participation, Surveys of Program Dynamics, American Community Surveys, the Business Register, and Economic Censuses and Surveys. With few exceptions, states have partnered with the Census Bureau to share data. As of December 2008, Connecticut, Massachusetts, New Hampshire and Puerto Rico have not signed a partnership agreement, while a partnership with the Virgin Islands is pending. LEHD's second method of developing employer-employee data relations through the use of federal tax data has been completed. LEHD has produced summary tables on accessions, separation, job creation, destruction and earnings by age and sex of worker by industry and geographic area. The data files consist of longitudinal datasets on all firms in each participating state (quarterly data, 1991- 2003), with information on age, sex, turnover, and skill level of the workforce as well as standard information on employment, payroll, sales and location. These data can be accessed for all available states from the Project Website. Data Availability: Research conducted on the LEHD data and other products developed under this proposal at the Census Bureau takes place under a set of rules and limitations that are considerably more constraining than those prevailing in typical research environments. If state data are requested, the successful peer-reviewed proposals must also be approved by the participating state. If federal tax data are requested, the successful peer-reviewed proposals must also be approved by the Internal Revenue Service. Researchers using the LEHD data will be required to obtain Special Sworn Status from the Census Bureau and be subject to the same legal penalties as regular Census Bureau employees for disclosure of confidential information. Basic instructions on how to download the data files and restrictions can be found on the Project Website. * Dates of Study: 1991-present * Study Features: Longitudinal * Sample Size: 48 States or U.S. territories

Proper citation: Longitudinal Employer-Household Dynamics (RRID:SCR_000817) Copy   

•   Source: SciCrunch Registry

http://wyss.harvard.edu/viewpage/594/

A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry.

Proper citation: Wyss Institute Imaging Core (RRID:SCR_000898) Copy   

•   Source: SciCrunch Registry

http://crag.uab.edu/crag/active.asp

Data set from a randomized controlled trial of cognitive interventions designed to maintain functional independence in elders by improving basic mental abilities. Several features made ACTIVE unique in the field of cognitive interventions: (a) use of a multi-site, randomized, controlled, single-blind design; (b) intervention on a large, diverse sample; (c) use of common multi-site intervention protocols, (d) primary outcomes focused on long-term, cognitively demanding functioning as measured by performance-based tests of daily activities; and (e) an intent-to-treat analytical approach. The clinical trial ended with the second annual post-test in January 2002. A third annual post-test was completed in December 2003. The area population and recruitment strategies at the six field sites provided a study sample varying in racial, ethnic, gender, socioeconomic, and cognitive characteristics. At baseline, data were collected by telephone for eligibility screening, followed by three in-person assessment sessions, including two individual sessions and one group session, and a self-administered questionnaire. At post-tests, data were collected in-person in one individual session and one group session as well as by self-administered questionnaire. There were four major categories of measures: proximal outcomes (measures of cognitive abilities that were direct targets of training), primary outcomes (measures of everyday functioning, both self-report and performance), secondary outcomes (measures of health, mobility, quality of life, and service utilization), and covariates (chronic disease, physical characteristics, depressive symptoms, cognitive impairment, psychosocial variables, and demographics). Phase I of ACTIVE was a randomized controlled, single-blind trial utilizing a four-group design, including three treatment arms and a no-contact control group. Each treatment arm consisted of a 10-session intervention for one of three cognitive abilities memory, reasoning, and speed of processing. Testers were blind to participant treatment assignment. The design allowed for testing of both social contact effects (via the contact control group) and retest effects (via the no-contact control group) on outcomes. Booster training was provided in each treatment arm to a 60% random subsample prior to first annual post-test. Phase II of ACTIVE started in July, 2003 as a follow-up study focused on measuring the long-term impact of training effects on cognitive function and cognitively demanding everyday activities. The follow-up consisted of one assessment to include the Phase I post-test battery. This was completed in late 2004.

Proper citation: Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) (RRID:SCR_000813) Copy   

•   Source: SciCrunch Registry