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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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The Surf-Hippo Neuron Simulation System Resource Report Resource Website 1+ mentions |
The Surf-Hippo Neuron Simulation System (RRID:SCR_007257) | data processing software, software resource, software application | The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux. | nif-0000-00170 | SCR_007257 | Surf-Hippo | 2026-08-12 10:49:43 | 1 | |||||||||||
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Cellpack Resource Report Resource Website 1+ mentions |
Cellpack (RRID:SCR_006831) | cellPack | data processing software, software resource, software application | A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA. | 3d packing software, pack, molecule, cell |
is related to: Autopack has parent organization: Autopack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151792 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006831 | 2026-08-12 10:49:32 | 9 | ||||||
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SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | data processing software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-08-12 10:49:11 | 325 | ||||||
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Western Australian State Agricultural Biotechnology Centre Resource Report Resource Website 1+ mentions |
Western Australian State Agricultural Biotechnology Centre (RRID:SCR_008577) | SABC | data or information resource, portal, software resource, organization portal | The SABC is the collaborative university Centre for R&D in agricultural and veterinary biotechnology in Western Australia. It provides platform technologies and world class equipment and facilities for R&D in agricultural biotechnology to researchers from universities, state government and industry. More than 20 research groups and companies rent space and use the SABC facilities. It is based at Murdoch University in Perth. Our Vision To be an eminent, internationally recognized centre for research and development in agriculture and veterinary biotechnology Our Mission To provide state-of-the-art facilities and equipment enabling multi disciplinary research in biotechnology which under pins the agricultural and veterinary industry, for the benefit of the community. This will be achieved by being recognised as the centre for agricultural biotechnology in WA providing national and international research links and collaborations fostering establishment of national centres in leading edge technologies Characteristics of the SABC * The SABC is a multi-user centre with a research spend of about $9 million pa * There is a critical mass of more than 225 researchers * The SABC combines university, state government and industry researchers in one cost-effective centre * The SABC operates as a ''Research Hotel'' in which different groups rent common laboratory space and access to platform technologies * The SABC supports incubation and co-location of new ag biotech companies in WA * The SABC promotes collaborative research, undertakes contract research, and provides many local, national and international linkages * SABC researchers are members of eight agricultural Cooperative Centres (CRCs) Research Focus The research focus is on molecular activities that involve or promote primary production of commercial livestock, crop plants or microbes, or their subsequent processing for added value. The SABC also supports research in biomedical sciences, and environmental biotechnology. Deliverables and Outcomes SABC researchers have an outstanding track record of outputs and outcomes. These include the provision of co-located, state-of-the art, well run platform technologies for all WA researchers plant breeding support leading to improved crop varieties (molecular markers, yield, resistance to diseases and pests, better quality, variety ID, diagnostics), improved productivity and health of livestock, and biomedical diagnostics. Facilities and platform technologies The SABC provides the most comprehensive set of equipment and facilities for biotechnology R&D in WA, with full facilities for: cell and molecular biology, robotics, high throughput agricultural genetic analyses and diagnostics, structural, comparative and functional genomics, microarray technologies, proteomics and mass spectroscopy and bioinformatics support via the (CBBC). Training and Mentoring The SABC plays a major role in advanced training in ag biotech. There are about 100 Honours and PhD students in the research complement. The SABC also runs a series of hands on short courses in molecular biology, gene mapping, diagnostics, proteomics and bioinformatics. In 2005 new postgraduate certificate and diploma courses on Application of Molecular Technologies was established at Murdoch University, run by internationally qualified SABC researchers. These provide advanced education at the Postgraduate Certificate, Diploma and MSc levels, for local and international participants. click here for details The SABC runs the following hands-on training workshops: * Introduction to Molecular Biology * Molecular Mapping Techniques in Diagnostic Biotechnology * High Throughput Genetic Analysis * Introduction to Proteomics * Advanced Proteomics * Bioinformatics (with the CBBC) Competitive Advantages The SABC: * combines crop, veterinary and biomedical research in biotechnology in one centre * is multidisciplinary and inclusive * provides enabling facilities, platform technologies and common laboratories * is highly cost effective Researcher Groups Using the SABC * Division of Health Sciences (Murdoch)/Veterinary Sciences * Division of Science and Engineering (Murdoch)/Biological Sciences and Biotechnology * UWA (Natural Resources and Agriculture, Biochemistry) * Curtin University (Molecular Biotechnology, Horticulture) * Edith Cowan University (Human Genetics) * WA Dept of Agriculture (animal, plant, microbial) * Fisheries * Perth Zoo * Plant Biotechnology Research Group * Australian Centre for Necrotrophic Fungal Pathogens (ACNFP) * Rumen Biotechnology * Centre for High Throughput Agricultural Genetic Analysis (CHAGA) * Veterinary Virology, Parasitology, Microbiology * Saturn Biotech Pty Ltd * Grain Biotech Australia Pty Ltd * Proteomics International * Lighthouse Laboratories Pty Ltd * ID PLUS Pty Ltd * Royal Perth Hospital * Fremantle Hospital * Australian Neuromuscular Research Institute (ANRI) Partnering Opportunities The SABC can provide full facilities for contract R&D, start up companies or co-location of existing companies in agricultural, veterinary and biomedical sciences via its incubation program. Contact the Director for further information. Partnering Needs Investors interested in commercializing outputs of SABC researchers. | has parent organization: Murdoch University; Perth; Australia | nif-0000-31479 | SCR_008577 | 2026-08-12 10:49:47 | 2 | ||||||||||
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Rick Hansen Institute Resource Report Resource Website 1+ mentions |
Rick Hansen Institute (RRID:SCR_008570) | RHI | data or information resource, database, portal, organization portal | Organization that facilitates spinal cord injury research and care. By accelerating the translation of discoveries and best practices into improved treatments, it aims to improve the lives of people living with SCI. | nonprofit, spinal, bone, cord, injury, canada, british columbia, international, registry | Canadian Government ; the Government of Canada through Western Economic Diversification ; Rick Hansen Foundation ; Rick Hansen ; the Governments of British Columbia ; Alberta ; Manitoba and Ontario |
nif-0000-31461 | SCR_008570 | 2026-08-12 10:49:51 | 8 | |||||||||
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LONI Inspector Resource Report Resource Website 1+ mentions |
LONI Inspector (RRID:SCR_004923) | LONI Inspector | data processing software, software resource, software application | A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. | analyze, dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155785 | http://www.nitrc.org/projects/inspector | http://www.loni.ucla.edu/Software/LONI-Inspector | SCR_004923 | 2026-08-12 10:49:04 | 3 | |||||
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University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility Resource Report Resource Website 1+ mentions |
University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility (RRID:SCR_022430) | TTAB | material storage repository, service resource, biobank, core facility, storage service resource, access service resource | Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams. | USEDit, ABRF, biorepository |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
ARBF_1435 | https://coremarketplace.org?citation=1&FacilityID=1435 | SCR_022430 | Tumor Tissue/Biospecimen Bank (TTAB), University of Pennsylvania Perelman School of Medicine Tumor Tissue/Biospecimen Bank (TTAB) | 2026-08-12 10:52:32 | 3 | |||||||
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PyFRAP Resource Report Resource Website 1+ mentions |
PyFRAP (RRID:SCR_022665) | data processing software, data analysis software, software resource, software application | Software Python package for FRAP analysis. Simulation based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. Used to assess molecular diffusion. | Fluorescence recovery after photobleaching, analyze FRAP experiments in 3D geometries, assess molecular diffusion, | Free, Available for download, Freely available | biotools:pyfrap | https://bio.tools/pyfrap | SCR_022665 | Python Fluorescence Recovery After Photobleaching | 2026-08-12 10:52:36 | 1 | ||||||||
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ANTS marking and analysis tools Resource Report Resource Website 1+ mentions |
ANTS marking and analysis tools (RRID:SCR_022543) | data processing software, data analysis software, software resource, software application | Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool. | marking ant motion trajectories, dataset from video, tracking performance evaluation | Free, Available for download, Freely available | SCR_022543 | ANTS_marking_and_analysis_tools | 2026-08-12 10:52:54 | 3 | ||||||||||
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PyFDAP Resource Report Resource Website 1+ mentions |
PyFDAP (RRID:SCR_022664) | data processing software, data analysis software, software resource, software application | Software tool as automated analysis of fluorescence decay after photoconversion (FDAP) experiments. | automated analysis of fluorescence decay, photoconversion experiments, FDAP | PMID:25380959 | Free, Available for download, Freely available | SCR_022664 | Python Fluorescence Decay After Photoconversion | 2026-08-12 10:52:46 | 1 | |||||||||
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Chemotaxis and Migration Tool Resource Report Resource Website 1+ mentions |
Chemotaxis and Migration Tool (RRID:SCR_022708) | data processing software, data analysis software, software resource, software application | Software tool for data analysis from time stack chemotaxis experiments. Based on NIH ImageJ image processing system. | time stack chemotaxis experiments data, time stack chemotaxis experiments analysis, chemotaxis experiments graphs, statistical analysis | Free, Available for download, Freely available | SCR_022708 | Chemotaxis and Migration Tool version 2.0 | 2026-08-12 10:52:55 | 7 | ||||||||||
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SwissDock Resource Report Resource Website 100+ mentions |
SwissDock (RRID:SCR_022564) | software resource, data access protocol, web service | Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS. | Protein small molecule docking, predict molecular interactions, target protein and small molecule interactions, | FNS 310030_130857; Swiss Institute of Bioinformatics |
PMID:21624888 | Free, Freely available | SCR_022564 | 2026-08-12 10:52:45 | 159 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data processing software, data analysis software, software resource, software application | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-08-12 10:52:46 | 20 | |||||||
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CORAL Resource Report Resource Website 50+ mentions |
CORAL (RRID:SCR_022711) | CORAL | data processing software, data analysis software, software resource, software application | Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis. | FAIR data, Contexton, Microtype, Data Management, Provenance, Data Analysis, Jupyter | has parent organization: University of California at Berkeley; Berkeley; USA | US Department of Energy | Free, Available for download, Freely available | SCR_022711 | Contextual Ontology based Repository Analysis Library | 2026-08-12 10:52:55 | 95 | |||||||
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SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data processing software, data analysis software, software resource, software application | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | 2026-08-12 10:52:37 | 13 | ||||||||
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University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) | CyTOF | material storage repository, service resource, core facility, storage service resource, access service resource | CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.� | USEDit, ABRF, stockroom | is listed by: ABRF CoreMarketplace | ARBF_1419 | https://coremarketplace.org?citation=1&FacilityID=1419 | SCR_022410 | University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center, IFI CyTOF Service Center | 2026-08-12 10:52:53 | 39 | |||||||
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AxonDeepSeg Resource Report Resource Website 1+ mentions |
AxonDeepSeg (RRID:SCR_022531) | segmentation software, image analysis software, software application, data processing software, software resource | Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks. | automatically segmenting axons and myelin sheaths, microscopy images | Canada Research Chair in Quantitative Magnetic Resonance Imaging ; Canadian Institute of Health Research ; Canada Foundation for Innovation ; Natural Sciences and Engineering Research Council of Canada ; TransMedTech ; Quebec BioImaging Network |
PMID:29491478 | Free, Available for download, Freely available | SCR_022531 | 2026-08-12 10:52:44 | 1 | |||||||||
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Bandage Resource Report Resource Website 10+ mentions |
Bandage (RRID:SCR_022772) | data processing software, data analysis software, software resource, software application | Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies. | interactive visualization, de novo genome assemblies, visualising de novo assembly graphs, analysing de novo assemblies |
is listed by: Debian is listed by: OMICtools |
PMID:26099265 | Free, Available for download, Freely available | OMICS_09013 | https://github.com/rrwick/Bandage, https://sources.debian.org/src/bandage/ | SCR_022772 | Bioinformatics Application for Navigating De novo Assembly Graphs Easily | 2026-08-12 10:52:56 | 27 | ||||||
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hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | data processing software, data analysis software, software resource, software application | Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning. | Error correction, read overlapping, hifiasm, haplotype resolved de novo assembler, PacBio Hifi reads | NHGRI R01HG010040; NHGRI U01HG010971 |
PMID:35534630 | Free, Available for download, Freely available | SCR_022771 | hifiasm_meta | 2026-08-12 10:52:37 | 2 | ||||||||
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Cell Morphology Labelling Tool Resource Report Resource Website 1+ mentions |
Cell Morphology Labelling Tool (RRID:SCR_022770) | image, data or information resource, data management software, software application, software resource, 3d spatial image | Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography. | LabelingTool, holotomography, 3D RI cell image, image quality, mange 3D RI cell images | has parent organization: Yonsei University; Seoul; South Korea | Free, Available for download, Freely available | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | SCR_022770 | 22CellMorphologyLabelingTool | 2026-08-12 10:52:47 | 1 |
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