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https://bioscience.lonza.com/lonza_bs/JP/en/Transfection/p/000000000000276883/4D-Nucleofector-X-Unit

One of four functional modules of 4D-Nucleofector System. It supports Nucleofection of various cell numbers cells in different formats.

Proper citation: Lonza: 4D Nucleofector X Unit (RRID:SCR_023155) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/50143210?SID=srch-srp-50143210

Storage used for high capacity random access storage (210 SBS microplates) at ambient conditions. The Cytomat 10 Hotel (PH) offers multiple transfer positions, dual access point (DAP) and as combined benchtop-under bench solution, it allows flexible placement within the laboratory.

Proper citation: Thermo Fisher: Cytomat 10 Hotel Ambient Storage (RRID:SCR_023273) Copy   

•   Source: SciCrunch Registry

https://www.questionpro.de/

Survey software to design and host questionaires. Used as survey creator. Enables to choose from survey question types ranging from net promoter score questions for efficient customer satisfaction surveys to advanced multiple-choice and logic-based research questions.

Proper citation: QuestionPro (RRID:SCR_023309) Copy   

•   Source: SciCrunch Registry

http://quantprime.mpimp-golm.mpg.de

Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes.

Proper citation: QuantPrime (RRID:SCR_015498) Copy   

•   Source: SciCrunch Registry

http://samurai-graph.sourceforge.jp/

Samurai Graph is a highly functional and user-friendly graph plotter. It can plot the graphs from the scalar to vector type 2-dimensional data. Samurai Graph is an open source development project, released under the GNU Lesser General Public License (LGPL). Samurai Graph is Java-based and platform-independent application. It runs on most major operating systems including MS-Windows, Linux, MacOS X, FreeBSD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Samurai Graph: A highly functional and user-friendly graph plotter (RRID:SCR_013594) Copy   

•   Source: SciCrunch Registry

http://www.vsh.com/products/mflt/index.asp

Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.

Proper citation: ModFit LT (RRID:SCR_016106) Copy   

•   Source: SciCrunch Registry

https://github.com/IGGoncalves/PhysiCOOL

Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects.

Proper citation: PhysiCOOL (RRID:SCR_023305) Copy   

•   Source: SciCrunch Registry

http://www.abbiotec.com/

An Antibody supplier

Proper citation: Abbiotec (RRID:SCR_013596) Copy   

•   Source: SciCrunch Registry

https://www.medicalexpo.com/ja/prod/erma/product-68401-922563.html

Automatic cell counting instrument. Used to count blood cells.

Proper citation: ERMA: Automatic blood cell counter PCE-210N (RRID:SCR_023148) Copy   

•   Source: SciCrunch Registry

https://github.com/AIRI-Institute/DeepCT

Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome.

Proper citation: DeepCT (RRID:SCR_023302) Copy   

•   Source: SciCrunch Registry

http://www.hematology.org/Publications/Videos/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. ASH's video library includes a number of films produced on various topics, including ASH''s history and award winners, Society programs such as the Clinical Research Training Institute, and a trailer and clips from the hematology documentary Blood Detectives, which aired on Discovery Health. These videos were created for educational purposes, and we encourage members of the hematology community to share them with others.

Proper citation: ASH Video Library (RRID:SCR_005777) Copy   

•   Source: SciCrunch Registry

http://microrna.osu.edu/.UCbase4

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. UCbase & miRfunc is a database of (i) human, mouse and rat microRNAs and (ii) Ultraconserved elements providing information about function, expression and correlation between these classes of non-coding RNAs and the disorders related to their aberrant expression. The genomics interface allows the user to explore where whole-genome collections of miRNAs and UCRs are located with respect to annotation sets such as band, disorders and known genes. The Blast interface provides a web tool for matching miRNAs/UCRs elements against any given sequence and providing specific functional information on the results. 481 Ultraconserved sequences (UCRs) longer than 200 bases were discovered in the genomes of human, mouse and rat. These are DNA sequences showing 100 percent identity among the human, mouse and rat genomes. UCRs are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas and in some instances regulated by microRNAs (miRNAs), the most extensively studied category of non-coding RNAs (ncRNAs). Here we present the first database which links UCRs and miRNAs with the related human disorders and genomic properties.

Proper citation: UCbase & miRfunc: Ultraconserved Sequences and miRNA Funciton Database (RRID:SCR_005771) Copy   

•   Source: SciCrunch Registry

http://www.plexdb.org/plex.php?database=Barley/funcexpression.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 11, 2012. FuncExpression is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase. Platform: Online tool

Proper citation: FuncExpression (RRID:SCR_005773) Copy   

•   Source: SciCrunch Registry

http://bigg.ucsd.edu/

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

Proper citation: BiGG Database (RRID:SCR_005809) Copy   

•   Source: SciCrunch Registry

http://the_brain.bwh.harvard.edu/uniprobe/

Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.

Proper citation: UniPROBE (RRID:SCR_005803) Copy   

•   Source: SciCrunch Registry

http://edwardslab.bmcb.georgetown.edu/downloads/

The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases.

Proper citation: Peptide Sequence Database (RRID:SCR_005764) Copy   

•   Source: SciCrunch Registry

http://mutationassessor.org/

A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MutationAssessor (RRID:SCR_005762) Copy   

•   Source: SciCrunch Registry

http://h-invitational.jp/varygene/

It consists of a Genome Browser, an LD Search System, and the VaryGene 2 system. The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes, while LDSearchSystem is a search system for linkage disequilibrium (LD) bins. VaryGene 2 is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. VaryGene 2 provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains. Users can search by polymorphisms, transcripts, STRs/SARs, and CNVs.

Proper citation: VarySysDB (RRID:SCR_005880) Copy   

•   Source: SciCrunch Registry

http://indel.bioinfo.sdu.edu.cn/gridsphere/gridsphere

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.

Proper citation: IndelFR - Indel Flanking Region Database (RRID:SCR_006050) Copy   

•   Source: SciCrunch Registry

http://www.utrome.org

This database is intended as a comprehensive resource for UTR (Untranslated Region) biology in C. elegans. The database provides detailed information on UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated as part of the NYU UTRome project (including preliminary characterization of UTR clones, USTs (UTR sequence tags), curated sequences, and computational and experimental analysis of functional elements). Examples of functional elements within UTRs include predicted and validated microRNA (miRNA) binding sites (responsible for post-transcriptional gene regulation), putative consensus signals for polyA addition, and predicted secondary structures (which may influence the biological activity of UTRs). The UTRome project is part of the ModEncode Consortium, an NIH initiative to characterize at a genomic scale functional sequence elements encoded in the worm (C. elegans) and fly (D. melanogaster) genomes. UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of UTRs we are building a UTR database for C. elegans.

Proper citation: UTRome.org (RRID:SCR_005878) Copy   

•   Source: SciCrunch Registry