Resources

Algae  |  Arabidopsis |  Archaea  |  Databases  |  E. coli  |  Facilities  |  General Information  |  Genomes  |  Maize  |  Metabolism  |  Protein Research  |  Research Integrity  |  Sequence Analysis Tools  |  Yeast

Algae

Bigelow National Center for Marine Algae and Microbiota | NCMA - Culturing Algae, Bacteria, Viruses, Growth Medium, Seawater, Make a Deposit or order by location, merchandise

UTEX Culture Collection of Algae - Algal products, services and resources. UTEX is a Non-Profit Organization whose principle financial support is obtained through the National Science Foundation, UT-Austin and sale of cultures.


Arabidopsis

Arabidopsis Information Resource (TAIR) - The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions.

SIGnAL: Salk Institute Genomic Analysis Laboratory - Arabidopsis thaliana Functional Genomic Resource Database : T-DNA, Full-length cDNA.

T-DNA Express: Arabidopsis Gene Mapping Tool (Salk Institute knockout collection) - T-DNA Express: Arabidopsis Gene Mapping Tool, Arabidopsis Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene Expression Atlas. Collection of Arabidopsis T-DNA/Ds, Full-length cDNA, Arabidopsis Gene Expression Database. Created and developed by Huaming Chen


Archaea

UCSC Archaeal Genome Browser - The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing).


Databases

AraCyc Database - Arabidopsis Metabolic Pathways: AraCyc Mirror

E. coli Database Collection (ECDC) - Welcome to ECDC. This collection offers you all information regarding the entire E.coli K12 chromosome we possibly could get. The collection is searchable in different ways: by a gen/sequence map, scrolling different tables or just by search for a keyword.

GENEVESTIGATOR (plant expression database) - GENEVESTIGATOR - The world's curated expression data at your fingertips

MaizeCyc Database - Metabolic Pathways in Maize or Corn

MaizeGDB - Genetics and Genomics Database - MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.

MetaCyc: Metabolic Pathways from all Domains of Life - MetaCyc is a highly curated metabolic database that contains metabolic pathways, enzymes, metabolites and reactions from all domains of life. MetaCyc contains 2453 pathways from 2788 different organisms.

Plant Expression Database (PlexDB) - PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Saccharomyces Genome Database (SGD) - The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.


E. coli

E. coli Database Collection (ECDC) - Welcome to ECDC. This collection offers you all information regarding the entire E.coli K12 chromosome we possibly could get. The collection is searchable in different ways: by a gen/sequence map, scrolling different tables or just by search for a keyword.


Facilities

DNA Facility - The Iowa State University DNA Facility in Ames Iowa provides Sanger sequencing, genomic or massively parallel DNA sequencing, oligo DNA synthesis and other biotechnology laboratory resource services for researchers in academia, industry and government.

Maize Genetics COOP Stock Center - A repository for maize mutants utilized by scientists conducting biological research. Order genetic stocks and obtain information about maize mutants.

National Plant Germplasm System - For ordering seeds from USFA collection


General Information

Chemical Reactivity Worksheet | response.restoration.noaa.gov - The Chemical Reactivity Worksheet (CRW) is a software program that can be used to find out about the chemical reactivity of thousands of common hazardous chemicals.

Cyberlipid Center (all about lipids) - All about lipids, their description, distribution, oxidation, analysis--Biology, medicine, nutrition, pharmacology--Resources for students, technicians, scientists--Publication news, events calendar, links.

GENEVESTIGATOR (plant expression database) - GENEVESTIGATOR - The world's curated expression data at your fingertips

IBS: Illustrator for Biological Sequences - In this work, we present a new tool called Illustrator for Biological Sequences (IBS) for assisting experimentalists in drawing publication-quality diagrams of both protein and nucleotide sequences. With a dual-mode user interface, experimentalists are allowed to produce their own schematic diagrams for either protein or nucleotide sequences in a convenient manner. To provide a user-friendly software package, abundant graphical elements, such as polygons, brackets, curves and polylines, are available for representing functional elements or regulatory molecules.

Interactive Plant Biology: A Kid's Guide to the Life Cycle of a Flower - ProFlowers Blog - Want to learn about flower life cycles? This article contains the facts about flowers in simple context for easy learning. Find your answers here.

Introduction to R Programming Online Course - DataCamp's Into to R training course teaches you how to use R programming for data science at your own pace with video tutorials & interactive challenges.

Keck Metabolomics Lab Instrument Availability & Reservations - Check availability of instruments in the W.M. Keck Metabolomics Research Laboratory, and submit reservations.

National Center for Biotechnology Information (NCBI) - The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

OpenWetWare (digital tools & resources) - OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. Learn more about us.
 If you would like edit access, would be interested in helping out, or want your lab website hosted on OpenWetWare, please join us. OpenWetWare is managed by the BioBricks Foundation.

Plant Expression Database (PlexDB) - PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Plant Stress - Information on impact, mitigation and updates on plant stressors: heat, cold, water logging, drought, salinity, mineral deficiency, mineral toxicity, oxidative stress and general stress

SDSC Biology Workbench - The Biology Workbench is a point and click interface for searching protein and nucleic acid sequence databases and for analyzing sequence data.

VirtualPlant 1.3 - VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.


Genomes

CoGe: Comparative Genomics - The CoGe Comparative Genomics Platform: a software suite of interlinked and interconnected web-based tools for easily visualizing, comparing, and understanding the evolution, structure and dynamics of genomes.

JGI Genome Portal (Joint Genome Institute) - The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility operated by Lawrence Berkeley National Laboratory (Berkeley Lab) and part of the Biosciences Area, is to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Berkeley Lab, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology.


Maize

Maize Genome Browser - Zea mays - Ensembl Genomes - Ensembl Plants is a genome-centric portal for plant species of scientific interest. Maize sequence and gene annotation from Maize Genome Sequencing project; BLAST against genome, download sequence sets, etc.

MaizeGDB - Genetics and Genomics Database - MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.

Panzea - Biology of Rare Alleles in Maize and its Wild Relatives: Maize genetic diversity, genetic mapping sets, bioinformatics software


Metabolism

AraCyc Database - Arabidopsis Metabolic Pathways: AraCyc Mirror

MaizeCyc Database - Metabolic Pathways in Maize or Corn

MetaCyc: Metabolic Pathways from all Domains of Life - MetaCyc is a highly curated metabolic database that contains metabolic pathways, enzymes, metabolites and reactions from all domains of life. MetaCyc contains 2453 pathways from 2788 different organisms.


Protein Research

Hampton Research Solutions for Crystal Growth - Crystallization products


Research Integrity

Research Misconduct (ISU resources) - A variety of resources that researchers and instructors may find useful when learning about or teaching about research misconduct.

The Lab: Avoiding Research Misconduct (interactive movie) - In "The Lab: Avoiding Research Misconduct," you become the lead characters in an interactive movie and make decisions about integrity in research that can have long-term consequences. The simulation addresses Responsible Conduct of Research topics such as avoiding research misconduct, mentorship responsibilities, handling of data, responsible authorship, and questionable research practices.


Sequence Analysis Tools

BLAST Phylogenetic Tree - Sequence Clean-up - Instructions to make phylogenetic trees with bootstrap values using the Iowa State University HPC system

ClustalW2 (Multiple Sequence Alignment) - ClustalW2 is a general purpose multiple (three or more) sequence alignment program for DNA or proteins. It attempts to calculate the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.

Eukaryotic Linear Motif (ELM) resource - This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction.

NetPrimer - Free primer analysis software. NetPrimer combines the latest primer analysis algorithms with a web-based interface allowing the user to analyze primers over the Internet.

Nucleotide BLAST - Align two or more sequences using BLAST.

Reverse Complement - Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. You may want to work with the reverse-complement of a sequence if it contains an ORF on the reverse strand.

Sequence Manipulation Suite - The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

Webcutter 2.0 - Mapping restriction enzymes sites


Yeast

Saccharomyces Genome Database (SGD) - The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.

Saccharomyces Yeast Deletion Project - The Saccharomyces Genome Project has revealed the presence of more than 6000 open reading frames (ORFs) in the S. cerevisiae genome. Approximately one third of these ORFs currently have no known function four years after their discovery. The goal of the Saccharomyces Genome Deletion Project is to generate as complete a set as possible of yeast deletion strains with the overall goal of assigning function to the ORFs through phenotypic analysis of the mutants.