Favourite Links (from Manish Raizada)Please also refer to the General Public Education tab A. News - Agriculture, Science and Engineering
A. News - Agriculture, Science and EngineeringNew Agriculturalist (Global Agriculture) AgricultureNews.com Agriculture 21 Magazine (FAO) BBC News Science/Nature SciTech Daily ScienceDaily SciCentral The Engineer Online News The Chronicle of Higher Education NSF Discoveries Science and International Development News
B. Reference ToolsLifeSciLink - Search Engine (journal databases, patents, grant abstracts) Web of Science (Guelph off-campus access) CiteULike – Share, store and organize articles (can upload and organize PDFs) BabelFish – Website language translation Delicious – organize your bookmarks online Faculty of 1000 – read what great scientists are reading Basic Statistics Online Statistics – note that Excel will do very sophisticated stats – search Excel Excel Tutorial on Statistics (also search Google for Excel statistics freeware) Journal Impact Factors Most Cited Researchers (ISI) Guelph CCS Software Downloads and Licenses MapMachine (National Geographic)
C. Molecular ToolsBLAST searching
C1. Molecular Sites with Great LinksPedro’s BioMolecular Tools BioWeb Pasteur Molecular toolbox at the European Bioinformatics Institute NCBI Tools for Data Mining Genamics SoftwareSeek ChemDex – Directory of Chemistry
C2. Specific Molecular ApplicationsNetPrimer Primo – PCR Primer design Tools (ChangBiosci) PCR Primer Design and Optimization – Excellent Online Lecture pDRAW – Free DNA Cloning and Vector Drawing Software (download) REBASE – Restriction Enzyme Database (take a tour) Obtain a virtual gel of digested bands from your sequence: List of all restriction enzymes (REBASE) Good online lecture on restriction enzymes Codon Usage Database (very useful when trying to express a transgene) Index of Plant Chromosome Numbers (Missouri Botanical Gardens) Animal Genome Size Database Plant Genome Size (Cot values) Database (Kew Gardens) WebElements Periodic Table – to remind yourself of basic chemistry
C3. Useful Molecular Software DownloadsProteinExplorer _ free software to view proteins in 3D STRAP – Structure Alignment Program for Proteins (free download) TreeFinder – to build phylogenetic trees (free download) ArgusLab – molecular modeling, graphics, drug design (free download) CHIME – free molecular visualization RasMol – molecular visualization freeware (download) Atlas of MacroMolecules – molecular molecules (including DNA, carbohydrates in 3D) ChemSketch – freeware to draw chemical structures
D.Protein, Enzyme and Proteomics LinksExPASy Expert Protein Analysis System Links: protein structure prediction, threading, making phylogenetic trees, finding protein targeting sequences, finding post-translational modification sequences: UniProt Database, the world’ s largest catalog of proteins: Introduction to Enzymes IUBMB Enzyme Nomenclature Database (for E.C. numbers) Enzyme Classification (E.C.) Tutorials Review of Primary, Secondary, Tertiary Protein Structure: Nice article on the importance of correct protein folding: Protein Databank (PDB) Database of 3D protein structures: SCOP (Structural Classification of Proteins) ProteinExplorer: free software to view proteins in 3D STRAP – Structure Alignment Program for Proteins (free download) Introduction to Protein Folding TargetP – Organelle targeting prediction ChloroP – Chloroplast targeting prediction iGAP: Proteome 3D protein structure and domain assignment. MIPS: Analysis and annotation of protein - contains software. AMPDB: Arabidopsis Mitochondrial Protein Database PlantsP: Plant protein phosphorylation database: Organelle DB: A database to proteins localized to organelles and subcellular AtNoPDB: Arabidopsis nucleolar protein database. PHYTOPROT: Clustering of plant proteins in families.
E. Favorite Maize LinksCIMMYT Corn Growers’ Handbook (Kingcorn) U.S. National Corn Growers’ Association Maize Genetics and Genomics Database (MaizeGDB) Ontario Corn Producers’ Association Maize Page, Iowa State University Food and Agricultural Organization Maize Query How a Corn Plant Develops (Iowa State) Click here for other maize links (from MaizeLink.org)…….
F. Links to Plant Genome Sequencing Project Databases1. General Genomics Glossary Genome News Network (see Quick Guide) TIGR Plant Genomics Projects MIPS (Arabidopsis, Maize, Medicago, Lotus, Rice, tomato) ENSEMBL (non-plant eukaryotic genomes) NCBI Plant Genomes 2. Arabidopsis TAIR Sequence Viewer TIGR Arabidopsis Genome Database MPSS - Arabidopsis small RNA Database Salk Institute Mapped TDNA Insertion Database Arabidopsis GDB (in development) 3. Rice TIGR Rice Genome Annotation Oryzabase 4. Maize (corn) 5. Comparative Grass Genomics Comparative Grass Genomics Centre (University of Georgia) GrainGenes - wheat and oat 6. Chlamydomonas Chlamydomonas DOE Joint Genome Institute 7. Poplar (tree) 8. Potato (and Solanaceae) 9. Tomato 10. Lotus japonicus (legume) 11. Medicago (alfalfa, legume) 12. Physcomitrella patens (moss) 13. Sorghum 14. Plant Genome Size (Cot values) Database (Kew Gardens) 15. Index of Plant Chromosome Numbers (Missouri Botanical Gardens)
G. Video Webcast Lectures in Biology, Genomics and Other Topics*****US National Institutes of Health Videocasts BioInteractive Online Lectures (Howard Hughes Medical Institute) *****Virtual Conference on Genomics and Bioinformatics Lectures (Advanced) *****Virtual Conference on Genomics and Bioinformatics Lectures ****NIH Proteomics Conference Webcasts (leaders in the field) *****NIH Chemistry and Biology Conference Webcasts (leaders in the field) Lectures In Medical Research (Howard Hughes Medical Institute) Lectures from 2003 Virtual Conference on Genomics and Bioinfomatics (Advanced) ****Genomics Lectures, techniques, proteomics (San Diego) (very authoritative) ****Bioinformatics Lectures, Univ of Michigan (Advanced) ***BBC News Go Digital Technology Video Archives *****Conversations with History (Videos) (University of California, Berkeley) *****MIT Lecture Videos (MIT World) ****University of California, Berkeley Webcasts and Podcasts ***UCLA Webcasts *****Research Channel Webcasts and Video Library ****United Nations Webcasts ***Rice University Webcasts ***University of California TV Podcasts *Georgetown University Webcasts and Podcasts (sociopolitical, economic) **Woodrow Wilson School of Public and International Affairs Webcasts (Princeton) Documentary, Educational and Lecture Videos (The Open Video Project) *****Library of 2500 Lectures on Global Health and Prevention (Global Health Network) ***Exploratorium Webcast Archive (interdisciplinary) UCLA Genome Ethics Lectures and Powerpoint Presentations ***Lectures on Genomics and Disease Prevention (CDC) *****Bioinformatics Math Video Lectures (MSRI) (Advanced) ******Cold Spring Harbor Webcasts of Pioneers of DNA Research *****Xerox Research Parc (Palo Alto, Silicon Valley) Video Archives Bioinformatics Seminars (World University Network) (Advanced) Biotech Channel Online Videos ***University of California, San Diego, Video Lecture Series Introduction to Bioinformatics and Genomics Course (CUNY) (Advanced) Microarray Outreach Slideshows (University of Vermont) Genomics and the Environment Slideshows (Advanced)
H. Metabolomics and Secondary Metabolism LinksAraCyc: A graphical representation of metabolic Pathways in Arabidopsis KEGG biochemical pathway database MetaCyc MapMan (for Arabidopsis) to associate biochemical pathways with Max Planck Institute for Molecular Plant Physiology Spice Plants (Spices Board of India) (scroll left column) Chemical Descriptions of Plant-Derived Scents and Flavors (FlavorNet) A Small Guide to Nature’s Fragrances (Bo Jensen) Natural Plant Medicines (not an endorsement) (PDR) Phytochemical and ethnobotanical database
I.Agriculture LinksNew Agriculturalist (Global Agriculture) AgricultureNews.com Agriculture 21 Magazine (FAO) *****Useful plants of the world (Australia) FAO Global Food Production Statistical Databases (FAOSTAT) New Crops (Purdue) FAO Waicent Portal – Links to all FAO Databases Directory of National Agricultural Research Institutions (FAO SDRR) ISNAR - List of Agricultural Research Organizations on the Web International Association of Agricultural Information Specialists SRISTI – Society for Research and Initiatives for Sustainable Technologies Consultative Group on International Agricultural Research (CGIAR) International Food Policy Research Institute Plants for a Future (edible, medicinal and useful plants)
J. Plant Biology LinksThe Arabidopsis Book Index of Plant Chromosome Numbers (Missouri Botanical Gardens) Animal Genome Size Database Plant Genome Size (Cot values) Database (Kew Gardens) *****Alphabetical List of Garden Plants, Common Name (Missouri Bot Garden) *****Alphabetical List of Garden Plants, Species Name (Missouri Bot Garden) Interesting Plants in the World’s Ecosystems (Missouri Botanical Garden) Links to Horticulture Basics and Plant Identification (Vocational Info Center) ***Plant Image Database (Missouri Botanical Gardens, TROPICOS) **General Botany, Systematics, Trees, Fungi (University of Wisconsin) Search Engine for Plants (Plant for a Future Database) Botany Courses of the Web Interesting Botanical Links (Scott’s Botanical links) ****Library of Crop Technology Animations ***Plant Anatomy (University of Hawaii Ethnobotany) Vascular Plant Image Database (Texas A&M University) **Vascular Plants of Ontario (University of Toronto) **Plant Phylogeny Database (Missouri Botanical Gardens) (Advanced)
K. International DevelopmentScience and International Development Developments – The International Development Magazine U.N. Millennium Project ***BBC Country Profiles ***The World Factbook (CIA) (Basic Nation Facts) The International Development Research Centre (IDRC) Canadian International Development Agency (CIDA) *****New Agriculturist (Global Agriculture Magazine) Gates Foundation The Rockefeller Foundation M.S. Swaminathan Research Foundation (India) International Food Policy Research Institute Consultative Group on International Agricultural Research (CGIAR) Grameen Bank for the Poor (Bangladesh) Development Gateway (DG Online Communities) http://developmentgateway.org/
L. Animations, Movies and Microscope Images*****Links to General Science Animations and Movies (North Harris College) *****DNA Molecular Animations (WEHI-TV) *****TimeLapse Movies of Plants (Plants in Motion, Prof. Roger Hangarter) ****Science Animations (Sumanas Inc) *****Biology Animations and Movies (North Harris College) Replication, Transcription, Translation Flash Animations (BioWeb) Molecular Biology Animation Library (Cold Spring Harbor Laboratory) ***Animation Comparison of Gene Versus a Chromosome (Cold Spring Harbor) Meiosis Animation (Dartmouth University) Nanoworld Image Database/XTALENT Image Gallery (Australia) Animations - Plant Life Cycles Life Cycle of a Moss Animation (Sumana Inc.) **Digital Morphology Images of Organisms (University of Texas, Austin) Introductory Biology Animations (University of Alberta) Plant Sucrose Transport Animation *Biochemistry Animations (Wiley) ****Energy Transfer Animation (University of Kansas Medical Center) *****Chemistry Animations (Iowa State University) ***Splicing DNA to Make Plasmid Constructs, Animation (Sumanas Inc) ***From the Universe to Inside a Plant Cell to an Electron (Molecular Expressions) **Shotgun DNA Sequencing Animation (JP Brody Lab, University of California, Irvine) Biology Flash Animations (JP Brody Lab, University of California, Irvine) Microarray Movie (GeneTraffic) Southern Blot Flash Video (Cold Spring Harbor, DNA Learning Center) http://www.dnalc.org/ddnalc/resources/shockwave/southan.html ****PCR Flash Animation (Cold Spring Harbor, DNA Learning Center) *****Microarray Flash Movie (Davidson College) ****Chemical Genetics Animations (Howard Huges Medical Institute ***Biology slides and animations (good collection from Univ of Hamburg)
M. Plant Movies and Images*****Fluorescent Images and Movies (Prof. Jim Haseloff, Cambridge University) Photographic Atlas of Plant Anatomy (University of Wisconsin) Slideshows in Plant Developmental Biology and Biotech (Jim Haseloff, Cambridge) *****Confocal 3D Movies of Arabidopsis (D.Ehrhardt, Stanford) (click on 3D Imaging) Plant Membrane Biology GFP Movies (Oxford Brookes University) Plant rhythms Using Luciferase (Andrew Millar, Warwick University) ****Oil Body GFP Movies (Maurice Maloney Lab, University of Calgary) ****Nuclear Dynamics in Arabidopsis Movies (David Galbraith, Mol Biol of the Cell J.) Chloroplast Stromule GFP Movies (Maureen Hanson Lab, Cornell) Plant Golgi GFP Movies (Chris Hawes, Oxford Brookes University) Plant Amyloplast Movies (Saito et al. Plant Cell) *****Plant Cell Type Movies (Donald Danford Plant Science Center) Maize Chromosome Bouquet Confocal Movies (Z.Cande Lab, Berkeley) |