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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Agilent 2100 Bioanalyzer Instrument Resource Report Resource Website 100+ mentions |
Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043) | instrument resource | Bioanalyzer system is automated electrophoresis tool that provides an analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats. | ABRF, bioanalyzer, electrophoresis, DNA, RNA, protein, data analysis, instrument, equipment | is listed by: USEDit | SCR_019389, Model_Number_2100 Bioanalyzer | https://www.agilent.com/cs/library/usermanuals/public/2100_Bioanalyzer_Expert_USR.pdf | SCR_018043 | Agilent 2100 Bioanalyzer, , 2100 Bioanalyzer (Agilent Technologies) | 2026-02-07 02:10:07 | 184 | ||||||||
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Sanford Burnham Prebys Medical Discovery Institute NMR Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute NMR Facility (RRID:SCR_014861) | instrument supplier, material resource | Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested. | facility, medical, nmr, protein, peptide, small molecules, carbohydrates, data collection, consultation, spectrometer, linux, software, analysis | Commercially available | SCR_014861 | SBP NMR Facility, SBP Medical Discovery Institute NMR Facility | 2026-02-07 02:16:10 | 0 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core (RRID:SCR_014862) | instrument supplier, material resource | Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy). | facility, la jolla, protein, analysis, quality control, molecular weight, stoichiometry | Commercially available | SCR_014862 | SBP Medical Discovery Institute Protein Analysis Core, SBP Protein Analysis Core | 2026-02-07 02:15:54 | 0 | ||||||||||
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Vilber E-BOX CX5 TS gel imager Resource Report Resource Website |
Vilber E-BOX CX5 TS gel imager (RRID:SCR_026106) | instrument resource | Stand alone gel imager for gel documentation. Provides high-resolution images of DNA, RNA or protein gels. Images can either be printed out directly or saved in internal storage. Transfer of data to PC is possible. | gel imager, gel documentation, images, DNA, RNA, protein, gels | Model_Number_ E-BOX_CX5_TS | SCR_026106 | E-BOX CX5 TS imager | 2026-02-07 02:17:06 | 0 | ||||||||||
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ALLSHENG Nano100 Micro-specrophotometer Resource Report Resource Website |
ALLSHENG Nano100 Micro-specrophotometer (RRID:SCR_026096) | instrument resource | Nano-100 microspectrophotometer to measure concentration of nucleic acid, protein and cell solution. 0.5 to 2μl of sample volume is required for each measurement. No cuvette is required. At the end of measurement, sample could be either wiped off directly or recovered with pipettor. | spectrophotometer, measure, absorbance, concentration, nucleic acid, protein, cell solution, | Model_Number_Nano100 | SCR_026096 | , Nano100 Micro-specrophotometer, Nano-100 micro-spectrophotometer | 2026-02-07 02:17:16 | 0 | ||||||||||
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BD Rhapsody Single-Cell Analysis System Resource Report Resource Website 1+ mentions |
BD Rhapsody Single-Cell Analysis System (RRID:SCR_027096) | instrument resource | System allows high-throughput capture of multiomic information from single cells using cartridge workflow and multitier barcoding system. Used for high-throughput, multiomic profiling of single cells. Allows to analyze gene expression at both mRNA and protein levels, as well as other cellular characteristics, using microwell-based system with multitiered barcoding approach.This enables the generation of various next-generation sequencing (NGS) libraries for deeper analysis. | profiling of single cells, analyze gene expression, mRNA, protein, multitiered barcoding, generation of next-generation sequencing libraries, | SCR_027096 | 2026-02-07 02:18:01 | 3 | ||||||||||||
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National Biomedical Center for Advanced ESR Technology Resource Report Resource Website 1+ mentions |
National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) | ACERT | biomedical technology research center, training resource | Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories. | electron spin resonance, spectrometer, electron spin resonance spectrometer, structure, dynamics, protein, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS P41GM103521; NCRR P41RR016292 |
Free, Freely Available | nlx_152669 | SCR_001444 | ACERT National ESR Center, National Biomedical Center for Advanced Electron Spin Resonance Technology | 2026-02-10 09:54:31 | 1 | ||||||
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BUSM Mass Spectrometry Resource Resource Report Resource Website |
BUSM Mass Spectrometry Resource (RRID:SCR_000823) | Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins. | systems biology technology center, mass spectrometry, glycoconjugate, oligosaccharide, protein | has parent organization: Boston University School of Medicine; Massachusetts; USA | NCRR P41RR010888 | nlx_152679 | SCR_000823 | Mass Spectrometry Resource for Biology and Medicine, Boston University School of Medicine Mass Spectrometry Resource, Boston University Mass Spectrometry Resource for Biology and Medicine | 2026-02-10 09:54:24 | 0 | |||||||
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Yeast Resource Center Resource Report Resource Website 1+ mentions |
Yeast Resource Center (RRID:SCR_007942) | YRC | biomedical technology research center, training resource | Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. | systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping | has parent organization: University of Washington; Seattle; USA | NCRR ; NIGMS P41 GM103533 |
nif-0000-03650 | SCR_007942 | YRC | 2026-02-10 09:55:44 | 6 | |||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-02-10 09:55:54 | 1 | |||||||
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Azure Biosystems c600 Imaging System Resource Report Resource Website |
Azure Biosystems c600 Imaging System (RRID:SCR_027952) | AZURE c600 | instrument resource | Benchtop instrument designed for life science research, specifically for imaging, detecting, and quantifying protein and nucleic acids on gels and blots. It enables multi-channel analysis, including laser infrared (IR) fluorescence, RGB visible fluorescence, and chemiluminescence, allowing for multiplexed Western blots. | imaging, detecting, quantifying, protein, nucleic acids, gels, blots | is related to: Azure 600 Western Blot Imaging System | Model_Number_Azure_c600 | SCR_027952 | , Azure c600 Imaging System, Azure c600 Western Blot Imaging System | 2026-02-10 09:59:27 | 0 | ||||||||
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MedScan Resource Report Resource Website 10+ mentions |
MedScan (RRID:SCR_003314) | data acquisition software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MedScan is a fast and flexible biomedical information extraction technology. It uses dictionaries to identify individual biomedical terms (proteins, cellular processes, small molecules, diseases, etc) referred to in literature articles, and applies advanced natural language processing techniques to detect the relationships within the article and extract these terms and the relationships; the overall process of detection, identification, extraction and assembling, is termed Information Harvesting. Information extracted by MedScan represents the multiple aspects of protein function, including protein modification, cellular localization, protein-protein interactions, gene expression regulation, molecular transport and synthesis, as well as association with diseases, and regulation of various cellular processes. This scope can be broadened by modifying information extraction rules and the dictionaries. Dictionaries can be assembled on any topic or area that is represented in the literature you wish to harvest. High-throughput data generation methodologies like microarray gene expression require new approaches for gathering information for data analysis. For the best results, computational approaches used for high-throughput data analysis require that biological information from the literature be a coherent and integrated part of the analysis software itself. Pathway Studio meets this challenge through its MedScan Technology and underlying ResNet database. All editions of Pathway Studio contain MedScan Technology to harvest information from the literature and to save this information in the Pathway Studio ResNet database ready for data analysis. MedScan is more than a web search engine. Indeed, the output of a Google search can be channeled into MedScan for example. Web searches, like Google, are excellent at finding items as a result of a query. A quick look at the output list usually locates the item for which you are looking. This approach however, is not well suited for information and knowledge gathering. Also, once information is gathered, where do you put it for later computational use? MedScan meets this challenge for the area of biomedical literature and biomedical online information. PubMed meets the needs for a central repository of biomedical literature. Researchers can go to PubMed and search for any topic and articles of interest, much like a web type of search. However, just like a web type of search, PubMed also provides a list of all the hits with a link to the articles. If a single article, or even just a few, are sought, this search approach is useful. Alternatively, MedScan will list all the articles of interest but additionally scans the text for relationships, highlights these relationships in the articles and then lists these relationships and the biological molecules and processes involved in the relationships in separate tables. The tables of relationships can be viewed graphically in Pathway Studio and can be saved into the ResNet database for use in experimental data analysis. | expression, function, article, biological, biomedical, cellular, dictionary, disease, information, literature, localization, medline interfaces, modification, molecule, process, protein, regulation, synthesis, technology, term, transport, FASEB list | PMID:15033866 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21259 | http://www.ariadnegenomics.com/products/medscan/reader/ | SCR_003314 | MedScan | 2026-02-11 10:56:41 | 37 | |||||||
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Human Gene and Protein Database (HGPD) Resource Report Resource Website 1+ mentions |
Human Gene and Protein Database (HGPD) (RRID:SCR_002889) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing. | gene, cdna clusters, cdnas, cdna sequences, human, in vitro, mrna varieties, protein, sds-page | has parent organization: National Institute of Advanced Industrial Science and Technology | PMID:22140100 PMID:19073703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02956 | SCR_002889 | HGPD | 2026-02-11 10:56:40 | 6 | |||||||
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Autophagy Database Resource Report Resource Website 10+ mentions |
Autophagy Database (RRID:SCR_002671) | Autophagy DB, AutophagyDB | data or information resource, database | Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. | autophagy, protein, homolog, ortholog, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:20972215 | Free, Available for download, Freely available | OMICS_03306, biotools:the_autophagy_database, r3d100012565 | https://bio.tools/the_autophagy_database https://doi.org/10.17616/R3J786 |
SCR_002671 | 2026-02-11 10:56:31 | 17 | |||||
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Jenalib: Jena Library of Biological Macromolecules Resource Report Resource Website 1+ mentions |
Jenalib: Jena Library of Biological Macromolecules (RRID:SCR_003031) | JenaLib | data or information resource, database | Database aimed at disseminating information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. The JenaLib intends to fulfill both scientific and educational needs. Authors who are willing to make available images or coordinates to the scientific community via the Image Library of Biological Macromolecules are requested to contact the author. A PDB/SWISS-PROT cross-reference database combines information from both PDB and SWISS-PROT, thus providing significantly more cross-references than either PDB or SWISS-PROT. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are supplemented by information on circular dichroism. | protein, nucleic acid, macromolecule, image, structure, rna, dan, carbohydrate, amino acid, nucleotide |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Nucleic Acid Database has parent organization: Fritz Lipmann Institute; Jena; Germany |
BMBF | PMID:11752308 PMID:10592237 PMID:8872391 |
Free, Freely available | nif-0000-03062 | https://jenalib.leibniz-fli.de/ | SCR_003031 | IMB Jena Image Library of Biological Macromolecules, Image library of biological macromolecules, Jena Library of Biological Macromolecules | 2026-02-11 10:56:37 | 1 | ||||
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SuperTarget Resource Report Resource Website 10+ mentions |
SuperTarget (RRID:SCR_002696) | SuperTarget | data or information resource, database | Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. | drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interaction |
is listed by: OMICtools has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
BMBF MedSys 0315450A; DFG RTG Computational Systems Biology GRK1772; DFG IRTG Systems Biology of Molecular Networks GRK1360; European Union SynSys ; NIGMS GM070064 |
PMID:22067455 PMID:17942422 |
Free, Freely available | r3d100012195, nif-0000-00416, OMICS_01591 | http://bioinf-tomcat.charite.de/supertarget/ http://bioinformatics.charite.de/supertarget https://doi.org/10.17616/R3TM0F |
SCR_002696 | 2026-02-11 10:56:32 | 28 | |||||
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CASBAH Resource Report Resource Website 1+ mentions |
CASBAH (RRID:SCR_002728) | CASBAH | data or information resource, database | Database which contains information pertaining to all currently known caspase substrates. | protein, caspase substrate, caspase |
is listed by: OMICtools has parent organization: Trinity College Dublin; Dublin; Ireland |
PMID:17273173 | OMICS_03304 | SCR_002728 | The CAspase Substrate dataBAse Homepage, The CASBAH, CAspase Substrate dataBAse Homepage | 2026-02-11 10:56:38 | 4 | |||||||
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RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq https://bio.tools/refseq https://doi.org/10.17616/R3HP70 |
SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-02-11 10:56:41 | 18049 | ||||||
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PRINTS Resource Report Resource Website 100+ mentions |
PRINTS (RRID:SCR_003412) | PRINTS | data or information resource, database | Compendium of protein fingerprints. Diagnostic fingerprint database. | compedium, protein, fingerprint, diagnostic, database, FASEB list | has parent organization: University of Manchester; Manchester; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03338 | http://130.88.97.239/PRINTS/index.php | SCR_003412 | 2026-02-11 10:56:44 | 395 | |||||||
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NCBI Taxonomy Resource Report Resource Website 100+ mentions |
NCBI Taxonomy (RRID:SCR_003256) | NCBI Taxonomy | data or information resource, database | Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such. | viroid, virus, nucleotide, protein, sequence, phylogeny, taxonomic, taxonomy, nomenclature, cladistics, classification, animal, genetic code, gold standard |
is used by: NIF Data Federation is used by: Vertebrate Taxonomy Ontology is listed by: re3data.org is related to: Taxonomy is related to: NEWT is related to: Phenoscape Knowledgebase is related to: EBIMed is related to: GOTaxExplorer is related to: Whatizit is related to: Integrated Manually Extracted Annotation has parent organization: NCBI is parent organization of: NCBITaxon |
PMID:18940862 PMID:18940867 |
Free, Freely available | nif-0000-03179, r3d100010776 | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html https://doi.org/10.17616/R3X039 |
SCR_003256 | NCBI Taxonomy Browser, Taxonomy Browser, Entrez Taxonomy Browser, NCBI Taxonomy Database | 2026-02-11 10:56:38 | 273 |
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