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http://amp.pharm.mssm.edu/archs4/

ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.

Proper citation: ARCHS4 (RRID:SCR_015683) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/Cuffmerge/3

The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.

Proper citation: Cuffmerge (RRID:SCR_015688) Copy   

•   Source: SciCrunch Registry

http://www.mightexsystems.com/family_info.php?cPath=245_347_346&categories_id=346

Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device.

Proper citation: Dynamic Spatial Illuminator Software (RRID:SCR_015725) Copy   

•   Source: SciCrunch Registry

https://ita.promega.com/products/fluorometers-luminometers-multimode-readers/multimode-readers/glomax_multi-detection-system/?catNum=E7061

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Glo-Max Multi Detection System (RRID:SCR_015575) Copy   

•   Source: SciCrunch Registry

https://github.com/iontorrent/TS

A variant vcf file analysis tool.

Proper citation: Torrent Variant Caller Standalone (RRID:SCR_015694) Copy   

•   Source: SciCrunch Registry

http://www.iitcinc.com/rotarod.html

Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard.

Proper citation: IITC Life Sciences: Rotarod Test (RRID:SCR_015698) Copy   

•   Source: SciCrunch Registry

https://www.visiopharm.com/solutions/oncotopix

Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.

Proper citation: Oncotopix Discovery (RRID:SCR_015690) Copy   

•   Source: SciCrunch Registry

http://www.neurocaregroup.com/dc-stimulator-neuroconn.html

Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology.

Proper citation: Neurocare: Neuroconn DC-Stimulator Plus (RRID:SCR_015520) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAHMS-SystemML/brahms

Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models.

Proper citation: BRAHMS (RRID:SCR_015642) Copy   

•   Source: SciCrunch Registry

https://compumedicsneuroscan.com/product/synamps-rt-64-channel-eeg-erp-ep-amplifier/

Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300.

Proper citation: Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) Copy   

•   Source: SciCrunch Registry

https://www.sigmaaldrich.com/US/en/products/labware/cell-culture-and-cryogenics/millicell-cell-culture-inserts-and-plates

Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides.

Proper citation: Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) Copy   

•   Source: SciCrunch Registry

http://autoprotocol.org/

Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation.

Proper citation: Autoprotocol (RRID:SCR_015764) Copy   

•   Source: SciCrunch Registry

https://www.olympus-lifescience.com/en/microscopes/inverted/ix53/

Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens.

Proper citation: Olympus IX-53 (RRID:SCR_015801) Copy   

•   Source: SciCrunch Registry

http://ced.co.uk/products/power3

Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control.

Proper citation: CED: Power1401 (RRID:SCR_016040) Copy   

•   Source: SciCrunch Registry

https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) Copy   

•   Source: SciCrunch Registry

http://www.funfaculty.org/

FUN is an international organization that is focused on neuroscience education and research at the undergraduate level. FUNs members and supporters include businesses and organizations; private liberal arts colleges, state and research university departments and programs; and individual faculty and students, all sharing a common interest in undergraduate neuroscience.

Proper citation: Faculty for Undergraduate Neuroscience (RRID:SCR_013536) Copy   

•   Source: SciCrunch Registry

http://www.aaas.org/

It is an international non-profit organization dedicated to advancing science around the world by serving as an educator, leader, spokesperson and professional association. In addition to organizing membership activities, AAAS publishes the journal Science, as well as many scientific newsletters, books and reports, and spearheads programs that raise the bar of understanding for science worldwide. :AAAS History: Founded in 1848, AAAS serves some 262 affiliated societies and academies of science, serving 10 million individuals. Science has the largest paid circulation of any peer-reviewed general science journal in the world, with an estimated total readership of one million. The non-profit AAAS is open to all and fulfills its mission to advance science and serve society through initiatives in science policy; international programs; science education; and more. For the latest research news, log onto EurekAlert!, the premier science-news Web site, a service of AAAS. :Membership and Programs: Open to all, AAAS membership includes a subscription to Science. Four primary program areas fulfill the AAAS mission: * Science and Policy * International Activities * Education and Human Resources * Project 2061 :AAAS Mission: AAAS seeks to advance science, engineering, and innovation throughout the world for the benefit of all people. To fulfill this mission, the AAAS Board has set these broad goals: * Enhance communication among scientists, engineers, and the public; * Promote and defend the integrity of science and its use; * Strengthen support for the science and technology enterprise; * Provide a voice for science on societal issues; * Promote the responsible use of science in public policy; * Strengthen and diversify the science and technology workforce; * Foster education in science and technology for everyone; * Increase public engagement with science and technology; and * Advance international cooperation in science. :

Proper citation: AAAS (RRID:SCR_013659) Copy   

•   Source: SciCrunch Registry

http://www.christopherreeve.org/

This foundation is dedicated to curing spinal cord injury by funding innovative research, and improving the quality of life for people living with paralysis through grants, information and advocacy.

Proper citation: Christopher and Dana Reeve Foundation (RRID:SCR_013550) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/Drugs/InformationOnDrugs/ucm129662.htm

Database that contains drug products approved on the basis of safety and effectiveness by the Food and Drug Administration.

Proper citation: Approved Drug Products with Therapeutic Equivalence Evaluations (RRID:SCR_013727) Copy   

•   Source: SciCrunch Registry

https://www.zotero.org

A software application that allows users to add and store research content directly from the web. Users can use the tool to add research content and bibliographic references directly to their Zotero library from their browser. The application stores PDFs, images, audio and video files, and snapshots of web pages on a single searchable interface.

Proper citation: Zotero (RRID:SCR_013784) Copy   

•   Source: SciCrunch Registry