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http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
http://www.broadinstitute.org/annotation/medea/
THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash.
Proper citation: MEDEA (RRID:SCR_013356) Copy
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
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
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
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
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
http://www.ncbi.nlm.nih.gov/refseq/rsg/
A data set of defined genomic sequences used as reference standards for well-characterized genes. These standard nucleotide sequences serve as foundations for locating mutations, establishing conventions for numbering exons and introns, and defining the coordinates of other variations. Sequences are aligned to reference chromosomes. RefSeqGene is a subset of NCBI RefSeq.
Proper citation: RefSeqGene (RRID:SCR_013787) Copy
http://www.ncbi.nlm.nih.gov/genome/viruses/
A database which provides viral and viroid genome sequence data and resource tools. Al viral genomes are downloadable and a complete RefSeq release of viral and viroid genome sequences are available.
Proper citation: NCBI Viral Genomes (RRID:SCR_013789) Copy
The NeuroML database is a curated relational database that provides for the storage and retrieval of computational neuroscience models expressed in NeuroML, which is an extensible XML-based language for describing complex mathematical models of neurons and neuronal networks. NeuroML models are unique in their modular and multi-scale structure, where subcomponents of models can correspond to neuroscience models. In particular, the NeuroML database allows for efficient searches over the components of models and metadata that are associated with a hierarchical NeuroML model description.
Proper citation: NeuroML Database (RRID:SCR_013705) Copy
http://www.ncbi.nlm.nih.gov/clone/
A database which integrates information about genomic clones and libraries, including sequence data, map positions and distributor information. A clone's standardized name in Clone DB is comprised of its microtiter plate address with plate number row and column, prefixed by the standard library abbreviation, to provide a unique clone name. Libraries with records may be accessed via the genomic or cell-based library browsers.
Proper citation: Clone DB (RRID:SCR_013791) Copy
Software package for editing and preparation of bitmap and vector graphics
Proper citation: Corel Graphics Suite (RRID:SCR_013674) Copy
A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials.
Proper citation: National Database for Clinical Trials related to Mental Illness (RRID:SCR_013795) Copy
https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy
https://drive.google.com/file/d/1hBdRU27fsVkioRZb_IY_8BGPwIi_2ipq/view?usp=drivesdk
Automated, high throughput microscale bioreactor system that replicates laboratory scale bioreactor performance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Thermo Fisher: Sartorius: Ambr 15 Cell Culture Generation 2 (RRID:SCR_013797) Copy
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