Curator Dashboard

You can use SMART in two different modes: normal or genomic.The main difference is in the underlying protein database used. In Normal SMART, the database contains Swiss-Prot, SP-TrEMBL and stable Ensembl proteomes. In Genomic SMART, only the proteomes of completely sequenced genomes are used; Ensembl for metazoans and Swiss-Prot for the rest.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

PRINTS is a compendium of protein fingerprints.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

• Resource
• SciCrunch
• 7 years ago - submitted by Jie Yang

Cloud based web platform connecting researchers, research organisations, funders and publishers in automated workflow management tool. Platform provides infrastructure for researchers, funders and publishers participating in Open Access Publishing. Features searchable database of journals compliant with research funders Open Access policies, connects researchers directly to journals submission systems, coordinates open access fee payments for funder with publisher upon acceptance, and supports compliancy by overseeing deposition of papers to designated repositories.

• Resource
• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Test to see if user receives RRID immediately at webpage after submission

• Resource
• dkNET
• 7 years ago - submitted by Ko-Wei Lin

Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.

• Resource
• NIF
• 7 years ago - by Anonymous

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

• Resource
• SciCrunch
• 7 years ago - submitted by William Thistlethwaite

Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.

• Resource
• SciCrunch
• 7 years ago - by Anonymous

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

• Resource
• SciCrunch
• 7 years ago - submitted by Eunjee Lee

Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous

Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous

Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous

Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.

• Resource
• SciCrunch
• 7 years ago - submitted by Anh Nguyet Vu

Mini Thermal Cycler PCR is compact thermal scanner, catalog number PTC-150 Cycler with Hot Bonnet heated lid for oil free cycling by MJ Research.

• Resource
• SciCrunch
• 7 years ago - by Anonymous

TGF-beta 1 (transforming growth factor beta 1) is one of three closely related mammalian members of the large TGF-beta superfamily that share a characteristic cystine knot structure (1‑7). TGF-beta 1, -2 and -3 are highly pleiotropic cytokines that are proposed to act as cellular switches that regulate processes such as immune function, proliferation and epithelial-mesenchymal transition (1‑4). Each TGF-beta isoform has some non‑redundant functions; for TGF-beta 1, mice with targeted deletion show defects in hematopoiesis and endothelial differentiation, and die of overwhelming inflammation (2). Human TGF‑ beta 1 cDNA encodes a 390 amino acid (aa) precursor that contains a 29 aa signal peptide and a 361 aa proprotein (8). A furin‑like convertase processes the proprotein to generate an N‑terminal 249 aa latency‑associated peptide (LAP) and a C‑terminal 112 aa mature TGF‑ beta 1 (8, 9). Disulfide‑linked homodimers of LAP and TGF‑ beta 1 remain non‑covalently associated after secretion, forming the small latent TGF‑ beta 1 complex (8‑10). Covalent linkage of LAP to one of three latent TGF‑ beta binding proteins (LTBPs) creates a large latent complex that may interact with the extracellular matrix (9, 10). TGF‑ beta is activated from latency by pathways that include actions of the protease plasmin, matrix metalloproteases, thrombospondin 1 and a subset of integrins (10). Mature human TGF‑ beta 1 shares 100% aa identity with pig, dog and cow TGF‑ beta 1, and 99% aa identity with mouse, rat and horse TGF‑ beta 1. It demonstrates cross‑species activity (1). TGF‑ beta 1 signaling begins with high‑affinity binding to a type II ser/thr kinase receptor termed TGF‑ beta RII. This receptor then phosphorylates and activates a second ser/thr kinase receptor, TGF‑ beta RI (also called activin receptor‑like kinase (ALK) ‑5), or alternatively, ALK‑1. This complex phosphorylates and activates Smad proteins that regulate transcription (3, 11, 12). Contributions of the accessory receptors betaglycan (also known as TGF‑ beta RIII) and endoglin, or use of Smad‑independent signaling pathways, allow for disparate actions observed in response to TGF‑ beta in different contexts (11).

• Resource
• SciCrunch
• 7 years ago - submitted by Jialei Duan