BIO 3012 - Research Methods
Biology Databases
Course guide for BIO 3012 Research Methods taught by Dr. John Murphy
Protocols/Trials
Qualitative Methods
Database Searching Techniques
Academic Citing & Writing
Biological Periodical and Specialized Databases/Portals/Search Engines/Tools
SBU Provided Periodical Databases
Featured Databases
Metadatabases/Portals
Protein Model/Protein Structure
Protein-Protein/Molecular Interactions
A to Z Journal Tracker
A list of digital periodicals (journals and/or magazines) available through University Libraries
A general database that contains information across a broad spectrum of academic disciplines.
Agriculture Collection
Comprised of 600+ titles, researchers have access to current and authoritative content that spans the agriculture industry and its related fields -- from practical aspects of farming to cutting edge scientific research in horticulture.
Annenberg Learner
These multimedia resources help teachers increase their expertise in their fields and assist them in improving their teaching methods. Many programs are also intended for students in the classroom and viewers at home. All Annenberg Learner videos exemplify excellent teaching.
Britannica Online: Academic Edition
This reference database combines the Encyclopædia Britannica, Merriam-Webster's Collegiate Dictionary & Thesaurus, magazines, periodicals, and many other research tools to provide users with a variety of reliable sources that students need to consult when conducting thorough research.
This is a quick tool to find an article when the citation is known. It will analyze the supplied information and create a menu of options based on the library's holdings.
EBSCO eBook Collection
This collection contains a large selection of multidisciplinary eBook titles representing a broad range of academic subject matter and is a strong complement to any academic collection. The breadth of information available through this package ensures that users will have access to information relevant to their research needs.
Environmental Studies and Policy Collection
Provides access to scholarly journals, magazines, and other reference sources covering environmental issues and policies. This database includes diverse perspectives from the scientific community, governmental policymakers, and corporate interests.
Environmental Studies In Context
Provides users with comprehensive information, empowering learners to critically analyze and understand important topics that affect people around the world. Integrating case studies, news, reference materials, academic journals, videos, and more, this resource helps users explore topics and events within Earth systems, global change, pollution, populations, and more.
Films on Demand
This video database allows streaming of educational videos directly online. Films on Demand is also fully searchable through University Libraries' catalog.
Gardening and Horticulture Collection
Focuses on the practical aspects and the scientific theory of horticulture studies. This database offers biotechnologists, farmers, hobbyists, and landscape architects access to important content relevant to their pursuits.
This database offers well-researched information covering all aspects of human impact to the environment. Its collection of scholarly, government and general-interest titles includes content on global warming, green building, pollution, sustainable agriculture, renewable energy, recycling, and more.
This is a growing interdisciplinary digital library of 12 million+ academic journal articles, books, and primary sources in 75 disciplines for scholars, researchers, and students.
MEDLINE (EBSCO Interface)
This database provides authoritative information on medicine, nursing, dentistry, veterinary medicine, the health care system, pre-clinical sciences, and much more. Created by the National Library of Medicine, MEDLINE uses MeSH (Medical Subject Headings) indexing with tree, tree hierarchy, subheadings, and explosion capabilities to search citations from 5,400+ current biomedical journals.
The National Library of Medicine created and maintains this resource to assist in locating authoritative health information. It contains carefully selected links to websites with health information on 900+ topics. The health topic pages include links to current news and related information. The A.D.A.M. medical encyclopedia brings health consumers an extensive library of medical images and videos, as well as 4,000+ articles about diseases, tests, symptoms, injuries, and surgeries.
MEDLINE with Full Text
MEDLINE with Full Text provides authoritative information on medicine, nursing, dentistry, veterinary medicine, the health care system, and pre-clinical sciences found on MEDLINE, as well as full-text for 1,470+ journals indexed in MEDLINE.
Open Access Theses and Dissertations
This website provides access to information about graduate theses and dissertations published around the world. Information about the theses comes from over 1000 colleges, universities, and research institutions. OATD currently indexes 2,220,740 theses and dissertations.
ProQuest Dissertations and Theses
This database is the world's most comprehensive collection of dissertations and theses from around the world, spanning from 1743 to the present day and offering full text for graduate works added since 1997, along with selected full text for works written prior to 1997.
Provides contextual information on hundreds of today's most significant science topics and showcases how scientific disciplines relate to real-world issues ranging from bacteria to obesity to weather. Integrates millions of full-text articles that include national and global publications, 200+ science experiments, 300+ interactive simulations, other multimedia, and top reference content.
This database provides access to 640+ science encyclopedias, reference books, and periodicals. Topics include biology, chemistry, earth and space science, environmental science, health and medicine, history of science, life science, physics, science and society, science as inquiry, scientists, and technology and wildlife.
This full-text scientific database offers journal articles and book chapters from 2,200+ active journals and 26,000+ books. Limit search results to content available through the University Libraries by selecting the Subscribed publications and Open Access articles check boxes.
ZFIN: The Zebrafish Model Organism Database
"The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data." -- Zebrafish Information Network (ZFIN)
Basic Local Alignment Search Tool (BLAST)
National Center for Biotechnology Information, U.S. National Library of Medicine
canSAR
"canSAR is an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions". --website
Neuroscience Information Framework (NIF)
ConsensusPathDB
"The use of ConsensusPathDB is free for academic users. ... ConsensusPathDB is being developed by the Bioinformatics group of the Vertebrate Genomics Department at the Max-Planck-Institute for Molecular Genetics in Berlin, Germany."--website
GQuery (Global Cross-database): Search NCBI databases
Enzyme Portal
The Enzyme Portal is for those interested in the biology of enzymes and proteins with enzymatic activity.
MOPED (Multi-Omics Profiling Expression Database)
PathogenPortal
Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute.
Pathway Commons
"Pathway Commons is a network biology resource and acts as a convenient point of access to biological pathway information collected from public pathway databases, which you can search, visualize and download. All data is freely available, under the license terms of each contributing database."-- "Pathway Commons is built and maintained by Memorial Sloan-Kettering Cancer Center and the University of Toronto."-- website
InterMine: Biological Data Warehouse
"InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools."--website
Nucleotide (National Library of Medicine)
The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
International Nucleotide Sequence Database Collaboration
The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI.
GeneCards: the Human Gene Compendium
"GeneCards is a searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes.GeneCards extracts and integrates gene-related data, including genomic, transcriptomic, proteomic, genetic, clinical, and functional information. This is automatically mined from >100 carefully selected web sources... Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science. Free for academic non-profit institutions."--website
UCSC Genome Bioinformatics
"This site contains the reference sequence and working draft assemblies for a large collection of genomes.
e!Ensembl
"The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. ... Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes."--website
e!EnsemblGenomes
The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institut
Vega Genome Browser
"A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.... Wellcombe Trust, Sanger Institute"--website
PATRIC (Pathosystems Resource Integration Center)
PATRIC is a NIH-NIAID -funded project of Virginia Tech's Cyberinfrastructure Division."
FlyBase
"FlyBase is supported by a grant from the National Human Genome Research Institute at the U.S. National Institutes of Health"--website
Support is also provided by the British Medical Research Council, the Indiana Genomics Initiative, and the National Science Foundation
through XSEDE resources provided by Indiana University
Gene Ontology Consortium
MGI (Mouse Genome Informatics)
JGI Genomes
A resource of te U.S. Department of Energy Joint Genome Institute (DOE JGI), provides databases of many eukaryote and microbial genomes.
RegulonDB
"RegulonDB is the primary database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions."-- website
Saccharomyces Genome Database
The SGD database is "the community resource for the budding yeast Saccharomyces cerevisiae."--website
"Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research." -- website
The SEED Viewer
"The SEED is a framework to support comparative analysis and annotation of genomes."--website
WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.
RGD (Rat Genome Database)
BioCyc Database Collection
"BioCyc is a collection of 3563 Pathway/Genome Databases (PGDBs), with tools for understanding their data."--website.
EnsemblFungi
Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data.
Cancer Genome Anatomy Project (National Cancer Institute)
EMAGE (e-Mouse Atlas of Gene Expression)
GreenPhyl
GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants.
Human Gene Mutation Database (HGMD®)
OrthoMaM
"The EnsEMBL database was used to decide on a set of 1-to-1 orthologous markers from those mammalian genomes available. Exons of reasonable length for further amplification from genomic DNA and sequencing in additional species were then selected. For phylogenomic purposes, CoDing Sequences (CDSs) were also collected. The phylogenetic utility and the evolutionary characteristics of these candidate markers were then evaluated using a homemade bioinformatics pipeline. The resulting OrthoMaM database can be interrogated through this website.
Netpath
NetPath is a manually curated resource of signal transduction pathways in humans. It is a collaborative effort between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics.
Reactome: a Curated Pathway Database
"REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases."--website
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
WikiPathways
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
MetaboLights
"MetaboLights is a database for Metabolomics experiments and derived information."--website
SMPDB (The Small Molecule Pathway Database)
ArrayExpress
"The database is a repository for functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are either submitted directly to ArrayExpress and curated by a team of specialist biological curators, or are imported systematically from the NCBI Gene Expression Omnibus database on a weekly basis."--website. MBL-EBI, Wellcome Trust Genome Campus
Gene Expression Omnibus
"GEO is a public functional genomics data repository supporting MIAME-compliant data submissions."--website.
maxd
"maxd is a data warehouse and visualisation environment for genomic expression data. It is being developed in the University of Manchester by the Microarray Bioinformatics Group."--website
Bgee: Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns between animal species."--website
Interferome
"This database will enable the reliable identification of an individual IRG or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements, chromosomal location and tissue expression of IRGs in human and mouse. This upgraded version, Interferome v2.0 has quantitative data, more detailed annotation and search capabilities and can be queried for one gene or thousands as in a gene list from a microarray experiment." -- website
Long Noncoding RNA Database v2.0: The Reference Database For Functional Long Noncoding RNAs
LncRNAdb is a database providing comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs). It is now currently maintained by the Genome Informatics Group
miRBase: the microRNA database
"The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)"--website
piRNABank
"piRNABank is a web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals namely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila. ... Copyright of Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, India"
Rfam
"The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs)"--website. European Molecular Biology Laboratory
Ribosomal Database Project (RDP)
"The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.... Center for Microbial Ecology, Michigan State University"--website
"A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data. ... SILVA uses a dual licensing model. In short, browsing and deploying the SILVA database."-- website
Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae: A comprehensive database of S. cerevisiae H/ACA and C/D box snoRNAs
This site is maintained by Wayne Decatur of the Fournier Lab in Department of Biochemistry and Molecular Biology.
SRPDB (Signal Recognition Particle Database)
RPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP. Christian Zwieb, Department of Biochemistry, University of Texas Health Science Center
tmRDB
The tmRDB is a tool in the study of the structures and functions of the tmRNA.
CATH / Gene3D
"CATH is a classification of protein structures downloaded from the Protein Data Bank. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor."--website by I. Sillitoe, T. Lewis, D. Lee, J. Lees, C. Orengo is licensed under a Creative Commons Attribution 4.0 International License.
Based on work at http://cath.biochem.ucl.ac.uk.
PDBsum Pictorial database of 3D structures in the Protein Data Bank
EMBL-EBI, Wellcome Trust Genome Campus, EBI is an outstation of the European Molecular Biology Laboratory
Protein Model Portal (PMP)
"PMP gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment." -- website.
RCSB PDB ( RCSB Protein Data Bank)
Research Collaboratory for Structural Bioinformatics (RCSB). An Information Portal to Biological Macromolecular Structures.
SCOP2
"SCOP2 is a successor of Structural classification of proteins (SCOP). Similarly to SCOP, the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Each node represents a relationship of a particular type and is exemplified by a region of protein structure and sequence ... This is a beta release and contains a fraction of protein structure data."--website
SCOP: Structural Classification of Proteins
SCOP was created in 1994 in the Centre for Protein Engineering and the Laboratory of Molecular Biology.
SWISS-MODEL
SWISS-MODEL is a fully automated protein structure homology-modelling server.
BioGRID: Biological General Repository for Interaction Datasets
"The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org)." --website.
CCSB Interactome Database
© CCSB Center for Cancer Systems Biology
Cell Collective
"The Cell Collective technology allows laboratory scientists working in different areas of the cell to collectively integrate their knowledge and create large-scale virtual cells in a non-technical fashion. ... The Cell Collective is free for academic use."--website
CIS-BP-RNA
"The Catalog of Inferred Sequence Binding Proteins of RNA (CISBP-RNA) is a library of RNA binding protein (RBP) motifs and specificities."--website
DIP: Database of Interacting Proteins
"The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions."--website.
iRefIndex
"A reference index for protein interaction data."-- website
RBPDB: RNA-binding Proteins Database
"RBPDB is a collection of RNA-binding proteins linked to a curated database of published observations of RNA binding."--website
STRING - Known and Predicted Protein-Protein Interactions
"STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations"--website
Copyright UCLA. The DIPTM database catalogs experimentally determined interactions between proteins.
InterPro: protein sequence analysis & classification
nterPro is a resource that provides functional analysis of protein sequences
OrthoMCL
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.
PEDANT 3 database - a Protein Extraction, Description and ANalysis Tool
A Munich Information Center for Protein Sequences/German Research Center for Environmental Health resource.
Pfam version 27.0 was produced at the European Bioinformatics Institute using a sequence database called Pfamseq, which is based on UniProt release 2012_06.
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. A University of Manchester resource.
PROSITE: Database of protein domains, families and functional sites
PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains.
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.
Limbform
"LimbformDB is an experiment-phenotype database of limb regeneration data published in the literature. Currently, it contains more than 800 different experiments." -- website
PhenomicDB
"PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms.
The inclusion of gene indices (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously.
PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene."--website
PHI-base: Pathogen Host Interactions
"PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base is therfore an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, PHI-base also includes antifungal compounds and their target genes."--website
PhytoPath
"PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource"--website
Planform
"PlanformDB is an experiment-phenotype database of planarian regeneration data published in the literature. Currently, it contains more than 1,000 different experiments."--website
FunSecKB
"The Fungal Secretome and Subcellular Proteome, i. e. protein subcellular location, KnowledgeBase (FunSecKB2) was created by Dr. Xiangjia (Jack) Min and John Meinken at Youngstown State University (YSU). It is an expanded version of a previous website built by Gengkon Lum. Dr. Min collected the data and designed the prediction algorithms. John Meinken implemented the database and built the website. Jessica Orr and Stephanie Frazier, undergraduate students, curated secreted proteins from recent literature. The work was supported by a grant from the YSU University Research Council and by a graduate assistantship for John Meinken from the YSU Center for Applied Chemical Biology. This server is supported by YSU."--website
Gelmap
Gelmap is a universal tool for spot visualization on a gel image. University of Hanover Proteomics Department
MetazSecKB (Metazoa (Human/Animal) Secretome and Subcellular Proteome KnowledgeBase)
"MetazSecKB is a knowledgebase for human/animal secretomes as well as human/animal proteins located in other subcellular locations. "--website
MitoMiner
MitoMiner is hosted and maintained by the Bioinformatics group at the MRC Mitochondrial Biology Unit. It is built using InterMine, a general purpose open-source data warehouse system. MitoMiner is hosted and maintained by the Bioinformatics group at the MRC Mitochondrial Biology Unit. It is built using InterMine, a general purpose open-source data warehouse system.
Plant Alternative Splicing Database
A Youngstown State University resource
PlantSecKB (Plant Secretome and Subcellular Proteome KnowledgeBase)
"The Plant Secretome KnowledgeBase (PlantSecKB) was designed by Dr. Xiangjia (Jack) Min, Gengkon Lum and John Meinken at Youngstown State University (YSU). Gengkon and John, MS graduate students, primarily implemeted the database. Jessica Orr and Stephanie Frazier, undergraduates, curated secreted proteins from recent literature. The work was supported by a grant from the Ohio Plant Biotechnoloy Consortium and a grant from the University Research Council, YSU. This server is supported by YSU."--website
Plasma Proteome Database (PPD)
"Plasma Proteome Database (PPD) was developed as a part of Human Proteome Organization's (HUPO) initial effort to characterize human plasma proteome. This is one of the largest resources on proteins reported in plasma and serum. PPD hosts qualitative and quantitative information on proteins (including those from MRM-based assays) reported in plasma and serum and hence serves as reference platform for biomarker discovery. In addition, proteins reported in extracellular vesicle isolated from plasma are also available."--website
PRIDE Archive - proteomics data repository
"The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence."--website. EMBL-EBI, Wellcome Trust Genome Campus. EBI is an outstation of the European Molecular Biology Laboratory
"UniGene computationally identifies transcripts from the same locus; analyzes expression by tissue, age, and health status; and reports related proteins (protEST) and clone resources. ... National Center for Biotechnology Information, U.S. National Library of Medicine"--website
Allen Brain Atlas Data Portal
"The Allen Mouse and Human Brain Atlases are projects within the Allen Institute for Brain Science which seek to combine genomics with neuroanatomy by creating gene expression maps for the mouse and human brain.."--Wikipedia 10/08/2014
Antibody Registry
"The Antibody Registry was created to give researchers a way to universally identify antibodies used in in the course of their research. The Antibody Registry assigns unique and persistent identifiers to each antibody so that they can be referenced within publications. Unlike antibody names or catalog numbers, these identifiers only point to a single antibody, so that the actual antibody used in your research research can be identified by humans and search engines.."--website
Barcode of Life Data Systems (BOLD Systems)
"The Barcode of Life Data Systems (BOLD) is an informatics workbench aiding the acquisition, storage, analysis, and publication of DNA barcode records. By assembling molecular, morphological, and distributional data, it bridges a traditional bioinformatics chasm. BOLD is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases."--website
Biodiversity Information Serving Our Nation (BISON)
From the website description: "The Core Science Analytics, Synthesis, and Libraries (CSAS&L) program of the U.S. Geological Survey (USGS) is developing Biodiversity Information Serving Our Nation (BISON), an integrated and permanent resource for biological occurrence data from the United States."
BioModels Database
"BioModels Database is a repository of computational models of biological processes. Models described from literature are manually curated and enriched with cross-references. All models are provided in the Public Domain. ... BioModels Database is developed by the BioModels.net team (part of the PST at EMBL-EBI, UK), the Le Novère lab (Babraham Institute, UK) and the SBML Team (Caltech, USA). "--website
bioMovies
"The bioMovies project is supported by: a Higher Education Academic Challenge Grant from the United States Department of Agriculture and the College of Agriculture and Life Sciences at NC State University. ... iteractive digital video for academic enviroments."--website
CellML
"CellML is an international collaborative initiative built around open source science and software. The cellml.org website is a community hub for all things CellML. This section contains information about projects, research groups and events within and related to the CellML community."--website
Clone DB
"The NCBI Clone DB replaces and expands upon the former NCBI Clone Registry, which was established during the era of the human and mouse genome projects to represent a broader range of eukaryotic organisms and clone types."--website
CTD Comparative Toxicogenomics Database
"CTD promotes understanding about the effects of environmental chemicals on human health by integrating data from curated scientific literature to describe chemical interactions with genes and proteins, and associations between diseases and chemicals, and diseases and genes/proteins."--website
Drug2Gene
"Drug2Gene reports relations between genes/proteins and drugs/compounds including bioactivity data where available. The data has been collected from 19 public databases and integrated to provide a 'one-stop shop' for identifying tool compounds for genes or finding all known targets of a drug. ... Copyright © Metalife AG."--website
"Dryad is a nonprofit repository for data underlying the international scientific and medical literature. ... Dryad is a nonprofit organization that provides long-term access to its contents at no cost to researchers, educators or students, irrespective of nationality or institutional affiliation. Dryad is able to provide free access to data due to financial support from members and data submitters. Dryad's DPCs are designed to sustain its core functions by recovering the basic costs of curating and preserving data. New innovations are enabled by research and development grants and by support from donors."--website
ExoCarta
"ExoCarta, an exosome database, provides with the contents that were identified in exosomes in multiple organisms."--website, . Dr. Suresh Mathivanan, Department of Biochemistry
La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria
EzBioCloud
"EzBioCloud is a portal and cloud computing service specially designed for researchers in the fields of biology, biotechnology and medical science."--website
FINDbase: Genome Variation Allele Frequencies Database Worldwide
"an online resource documenting frequencies of pathogenic genetic variations leading to inherited disorders in various populations worldwide. The initial data came from previously published reports as well as from unpublished information contributed from individual researchers prior of publication. ... Data content is freely available to the public and there are no registration requirements for data querying."--website
Minimotif Miner (MnM)
"Minimotif Miner (MnM) analyzes protein queries for the presence of short contiguous peptide motifs that have a known function in at least one other protein (Minimotifs), Minimotif functions include posttranslational modification of the minimotifs (PTM), binding to a target protein or molecule, and protein trafficking. One major limitation in MnM and other minimotif prediction approaches is that "false positive" minimotifs result from the relatively low sequence complexity of the sequence definition. MnM 3.0 uses a rich semantic model and trained algorithm to reduce false positive predictions. When tested on a large test dataset 39% of validated minimotifs were recovered with all false positives eliminated. This is set as the default filter on MnM 3.0. We suggest that the known biology of the protein query and be used in selecting minimotifs for experimental study."--website
OpenAlex
"OpenAlex is a fully open catalog of the global research system. It's named after the ancient Library of Alexandria" -- docs.openalex.org
PortEco: EcoliWiki
"Our goal for EcoliWiki is to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements." -website
RTPrimerDB
"RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories."--website. Ghent University
SABIO-RK: Biochemical Reaction Kinetics Database)
"SABIO-RK is a curated database containing structured information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context."--website
Selectome: a Database of Positive Selection
"Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment. ... Department of Ecology and Evolution, Biophore, Lausanne University, CH-1015 Lausanne, Switzerland"--website
The Singapore Human Mutation And Polymorphism Database
"This website has been created to provide clinicans and scientists access to a central genetic database for the local population. The existence of population and country-specific databases is very important and valuable for the study of population history, genetic-testing, as well as disease association studies. The availability of allele and genotype frequencies for specific ethnic groups in our population would be useful for the selection of informative genetic markers in association studies involving complex traits or phenotypes. Thus, these led to the creation of this database which contains the allele and genotype frequencies. "--website
TreeFam - Database of Animal Gene Trees
"TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes. ... EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire"--website
Selected Open Access Journals
AMEDEO Literature Guide
"AMEDEO's core components include weekly emails with bibliographic lists about new scientific publications, personal Web pages for one-time download of available abstracts... and an overview of the medical literature published in relevant journals over the past 12 to 24 months"-- Website. A number of pharmaceutical companies sponsor some AMEDEO topics.
DOAJ (Directory of Open Access Journals)
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URL: https://libguides.sbuniv.edu/bio3012researchmethods
Subjects: Agriculture, Biology
Tags: qualitative research, quantitative research, research design, research methods, research protocols