Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology

Nikolau Group Research Resources

Questions or comments?

Contact us at nikolau.research@iastate.edu

Research Resources

Research integrity:

The Lab: Avoiding Research Misconduct (interactive movie)
http://ori.hhs.gov/thelab
Research Misconduct (ISU resources)
http://www.vpresearch.iastate.edu/en/for_researchers/research_misconduct/

General information:

Cyberlipid Center (all about lipids)
http://www.cyberlipid.org/index.htm
Genevestigator (plant expression database)
https://www.genevestigator.com/gv/index.jsp
Interactive Plant Biology: A Kid's Guide to the Life Cycle of a Flower
http://www.proflowers.com/guide/interactive-plant-biology-kids-guide-life-cycle-flower
Introduction to R
https://www.datacamp.com/courses/introduction-to-r
Keck Metabolomics Lab Instrument Reservations
http://www.metabolomics.biotech.iastate.edu/availability.html
National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov/
The Next Generation Biology Workbench (swami)
http://www.ngbw.org/
Plant Stress
http://www.plantstress.com/Articles/index.asp
PlexDB (plant - and some pathogens - gene expression site)
http://www.plexdb.org
San Diego Supercomputer (SDSC) Biology Workbench
http://workbench.sdsc.edu/
VirtualPlant (genomic data integration)
http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/
Writing

http://www.nature.com/naturejobs/2011/110707/full/nj7354-129a.html

Arabidopsis:

The Arabidopsis Information Resource (TAIR)
http://www.arabidopsis.org
Salk Institute Genomic Analysis Library (SIGnAL)
http://signal.salk.edu/
T-DNA Express: Arabidopsis Gene Mapping Tool (Salk Institute knockout collection)
http://signal.salk.edu/cgi-bin/tdnaexpress?GENE=at2g02990&FUNCTION=&TDNA
Arabidopsis Metabolomics Consortium
http://tht.vrac.iastate.edu:81/index.php
100 Ways to (try to) Grow Arabidopsis
http://www.hort.purdue.edu/hort/facilities/greenhouse/101exp.shtml

Maize:

Maize Genome Browser (Maize sequence and gene annotation from Maize Genome Sequencing project; BLAST against genome, download sequence sets, etc.)
http://www.maizesequence.org/index.html
Maize Genetics and Genomics Database
http://http://www.maizegdb.org/
Panzea (Maize genetic diversity, genetic mapping sets, bioinformatics software)
http://www.panzea.org/index.html

Algae:

CCMP - The Provasoli-Guillard National Center of Marine Phytolankton
https://ccmp.bigelow.org/
UTEX The Culture of Algae
http://www.sbs.utexas.edu/utex/

Yeast:

Yeast Genetics Stock Center Catalog (useful classical genetics protocols)
http://www.atcc.org/Portals/1/Pdf/ygsccatalog.pdf
Saccharomyces Genome Database

http://www.yeastgenome.org/
Stanford Yeast Deletion Project Overview
http://www-sequence.stanford.edu/group/yeast_deletion_project/project_desc.html#top

E. coli:

E. coli Community
http://www.ecolicommunity.org/
E. coli Database Collection (ECDC)

http://www.uni-giessen.de/ecoli/ECDC/ecdc.htm
E. coli Genotypes
http://ecoli.aist-nara.ac.jp/GB5/search.jsp
Genome Analysis Project in Japan
http://ecoli.aist-nara.ac.jp/GB5/search.jsp

Metabolism:

AraCyc
http://www.arabidopsis.org/biocyc/index.jsp
MaizeCyc
http://pathway.gramene.org/gramene/maizecyc.shtml
MetaCyc
(database of nonredundant, experimentally elucidated metabolic pathways)
http://www.metacyc.org/

Genomes:

CoGe (comparative genomics platform)
http://genomevolution.org/CoGe
JGI
(Joint Genome Institute)
http://genome.jgi-psf.org

Archaea:

UCSC Archaeal Genome Browser
http://archaea.ucsc.edu/index.html?org=Methanosarcina+acetivorans&db=metAce1&hgsid=291363

Sequence analysis tools:

BLAST (BLAST 2 sequences)
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=blast2seqClustalW2 (multiple sequences alignment)
http://www.ebi.ac.uk/Tools/clustalw2/index.html
Eukaryotic Linear Motif resource
http://elm.eu.org
Reverse Complement (reverse DNA sequence)
http://www.bioinformatics.org/sms/rev_comp.html
Premier Biosoft International (check primers quality)
http://www.premierbiosoft.com/netprimer/index.html
WebCutter (mapping restriction enzymes sites)
http://rna.lundberg.gu.se/cutter2/
Sequence Manipulation Suite (DNA manipulation tools)
http://www.ualberta.ca/~stothard/javascript/index.html

Facilities:

Maize Genetics Cooperation Stock Center (searching/ordering genetic stocks)
http://maizecoop.cropsci.uiuc.edu
W.M. Keck Metabolomic Research Lab
(availability calendars)
http://www.metabolomics.biotech.iastate.edu/availability.html
DNA Facility
http://www.dna.iastate.edu/
National Plant Germplasm System (for ordering seeds from USDA collection)
http://www.ars-grin.gov/npgs/

Protein research:

Protein Hydrophobicity Plots

http://arbl.cvmbs.colostate.edu/molkit/hydropathy/index.html
Hampton Research Solutions for Crystal Growth
http://hamptonresearch.com/Default.asp