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http://sourceforge.net/projects/niftysim/

A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages.

Proper citation: NiftySim (RRID:SCR_006591) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/LexEVS/LexGrid

LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: LexGrid (RRID:SCR_006627) Copy   

•   Source: SciCrunch Registry

http://www.alexaplatform.org/alexa_seq/index.htm

A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''.

Proper citation: ALEXA-Seq (RRID:SCR_006700) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/splicegrapher/

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

Proper citation: SpliceGrapher (RRID:SCR_006657) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

Proper citation: ChIPXpress (RRID:SCR_006653) Copy   

•   Source: SciCrunch Registry

https://www.promega.com/

An Antibody supplier

Proper citation: Promega (RRID:SCR_006724) Copy   

•   Source: SciCrunch Registry

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

Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function.

Proper citation: Web Game for Collaborative Labeling (RRID:SCR_006685) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/softsearch/

A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc).

Proper citation: SoftSearch (RRID:SCR_006683) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/GREC/

A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format

Proper citation: GREC Corpus (RRID:SCR_006719) Copy   

•   Source: SciCrunch Registry

https://www.med-associates.com/product/deluxe-behavioral-test-package/

Operant behavior test package for rat built to meet needs of research studies requiring additional reward and stimulus flexibility. One of Med Associates, Inc. operant conditioning and general behavior product.

Proper citation: Med Associates: Deluxe Behavioral Test Package with Rat Modular Chamber (RRID:SCR_021938) Copy   

•   Source: SciCrunch Registry

https://www.sdu.dk/en

University has campuses located in Southern Denmark and on Zealand with main campus in Odense and regional campuses in Slagelse, Kolding, Esbjerg and Sønderborg. University offers joint programes in co-operation with University of Flensburg and University of Kiel.

Proper citation: University of Southern Denmark; Denmark (RRID:SCR_021943) Copy   

•   Source: SciCrunch Registry

https://www.alveolelab.com/our-products/leonardo-photopatterning-software/

Photopatterning software to control PRIMO system including UV illumination module, microscope, camera and stage, and to precisely define experimental conditions.Used to design your own micropatterning manipulations.

Proper citation: Alveole Leonardo (RRID:SCR_021940) Copy   

•   Source: SciCrunch Registry

https://www.alveolelab.com/our-products/primo-micropatterning/

Photopatterning device for performing micropatterning, microfabrication and hydrogel polymerization.Part of PRIMO system.

Proper citation: Alveole: PRIMO photopatterning module (RRID:SCR_021941) Copy   

•   Source: SciCrunch Registry

https://biomedical-instruments.com/pdf/Narishige%20PC-10.pdf

Vertical pipette puller to create microelectrodes from borosilicate capillaries.

Proper citation: Narishige: PC 10 Puller (RRID:SCR_022057) Copy   

•   Source: SciCrunch Registry

https://www.zeitz-puller.com/

Horizontal pipette puller to pull and polish microelectrodes from borosilicate capillaries.

Proper citation: Zeitz: DMZ Universal Electrode Puller (RRID:SCR_022056) Copy   

•   Source: SciCrunch Registry

https://biomedical-instruments.com/pdf/Narishige%20MF-830.pdf

Powerful microscope mounted to produce microelectrodes for patch clamping.

Proper citation: Narishige: MF 830 Microgrinder (RRID:SCR_022055) Copy   

•   Source: SciCrunch Registry

https://www.onsetcomp.com/products/software/bhw-pro-dld/

Weather data logging software used for all HOBO data loggers and wireless data nodes. Used to read out and plot data, and export to spreadsheets for further analysis.

Proper citation: HOBOware Pro (RRID:SCR_021915) Copy   

•   Source: SciCrunch Registry

http://www.mrivideo.com/visuastimdigital.php

Audio visual stimulation system for functional MRI (fMRI) applications.

Proper citation: Resonance Technology: VisuaStimDigital (RRID:SCR_021892) Copy   

•   Source: SciCrunch Registry

https://support.izon.com/qnano-control-suite-software

Data acquisition software. Allows raw or filtered measurement data to be viewed in real time. Part of qNano system. Izon Control Suite Software V3.4 is maintenance software release that updates Izon current software.

Proper citation: Izon Control Suite (RRID:SCR_021922) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/t100-thermal-cycler?ID=LGTWGIE8Z

Small compact 96well thermal cycler. PCR system features intuitive touch screen and thermal gradient technology to optimize reaction in single run.

Proper citation: Bio-Rad: T100 Thermal Cycler (RRID:SCR_021921) Copy   

•   Source: SciCrunch Registry