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http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry
  

http://www.genemed.com/

A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization.

Proper citation: Genemed (RRID:SCR_000070) Copy   

•   Source: SciCrunch Registry
  

http://www.cogsci.ucsd.edu/media/uploads/grad/grad_fellowship_info.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This resource is a frequently updated listing of graduate student in cognitive science fellowship opportunities. For current opportunities, please see the PDF document.

Proper citation: University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities (RRID:SCR_000105) Copy   

•   Source: SciCrunch Registry
  

http://www.nationalmssociety.org/index.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward.

Proper citation: National MS Society (RRID:SCR_000104) Copy   

•   Source: SciCrunch Registry
  

http://www.gobics.de/fabian/treephyler.php

A software tool for fast taxonomic profiling of metagenomes.

Proper citation: Treephyler (RRID:SCR_000109) Copy   

•   Source: SciCrunch Registry
  

http://toc.lbg.ac.at/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.

Proper citation: Ludwig Boltzmann Cluster Translationale Onkologie (RRID:SCR_000020) Copy   

•   Source: SciCrunch Registry
  

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Proper citation: FastQ Screen (RRID:SCR_000141) Copy   

•   Source: SciCrunch Registry
  

http://www.ufl.edu/

Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences.

Proper citation: University of Florida; Florida; USA (RRID:SCR_000145) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html

Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

Proper citation: GenomicRanges (RRID:SCR_000025) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

Software that establishes a bridge between GEO and BioConductor.

Proper citation: GEOquery (RRID:SCR_000146) Copy   

•   Source: SciCrunch Registry
  

http://neuro.med.cornell.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages.

Proper citation: Neuroscience Link List (RRID:SCR_000130) Copy   

•   Source: SciCrunch Registry
  

https://compneuroweb.com/

Annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.

Proper citation: Computational Neuroscience on the Web (RRID:SCR_000010) Copy   

•   Source: SciCrunch Registry
  

http://jchempaint.github.io/

Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).

Proper citation: JChemPaint (RRID:SCR_000095) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BenLangmead/bsmooth-align

Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

Proper citation: BSmooth-align (RRID:SCR_000013) Copy   

•   Source: SciCrunch Registry
  

https://github.com/obophenotype/porifera-ontology

An ontology covering the anatomy of Porifera (sponges).

Proper citation: Porifera Ontology (RRID:SCR_000134) Copy   

•   Source: SciCrunch Registry
  

http://www.uu.nl/faculty/veterinarymedicine/EN/labs_services/CCI/Documents/Instructie%20Leica%20DMRE%20fluorescentie%20microscoop.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Microscope that enables bright field and fluorescence imaging options.

Proper citation: Leica: DMRE Fluorescence Microscope (RRID:SCR_000011) Copy   

•   Source: SciCrunch Registry
  

http://srf.sourceforge.net/

A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.

Proper citation: Sequence Read Format (RRID:SCR_000132) Copy   

•   Source: SciCrunch Registry
  

http://www.epilepsygenetics.eu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EPIGEN (RRID:SCR_000093) Copy   

•   Source: SciCrunch Registry
  

http://www.gbiosciences.com/default.aspx

Commercial antibody supplier that provides research materials for projects such as: protein purification, protein analysis, protein estimation assays, DNA purification, plasmid DNA isolation and transformation, protein quantification assays, and coupled assays for methylation. This supplier also provides buffers, reagents, education programs, and training programs.

Proper citation: G Biosciences (RRID:SCR_000007) Copy   

•   Source: SciCrunch Registry
  

http://dock.compbio.ucsf.edu/

An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design.

Proper citation: DOCK (RRID:SCR_000128) Copy   

•   Source: SciCrunch Registry