Takaisin Ajatusvarikolle - Back to the Thought Deposit
HAASTE - CHALLENGE
Dinoglyyfit
- Dinoglyfs - Esihistorialliset eläimet historiankirjoissa - Prehistoric Creatures Documented by the Ancient Man

Bookmarks
Bookmarks
Bookmarks
Bioinformatics
Bioinformatics
Bioinformatics

Artificial Intelligence
 Bayesian Networks
Biosurveillance
Causal Modelling and Discovery
Clinical Information Systems
Cognitive Science
Computational Biology/Bioinformatics
Consumer Health
Data Mining
Databases and Registries
Decision Support Systems
Decision Theory and Analysis
Dental Informatics
Disease Surveillance and Epidemiology
Education and Curricula
Expert Systems
Evidence-based Medicine and Meta-Analysis
Evaluation Methods
Functional Genomics
Gene Regulation Pathways
Graphics and Visualization
Health Economics
Health Services Research
Human-Computer Interaction
Image Analysis
Information Retrieval
Knowledge Representation
Machine Learning
Medical Errors
Medical Imaging
Metabolic Networks
Microarray Analysis
Modelling (Physiologic and Anatomic)
Natural Language and Text Processing
Neural Networks
Neuroinformatics
Nursing Informatics
Ontology Development
Organizational Theory
Patient Safety
Phylogenetic Trees
Physiologic Monitoring
Planning
Public Health Informatics
Qualitative Evaluation
Sequence Analysis
Signal Transduction Networks
Simulation
Social and Cultural Factors
Standards Development
Structural Informatics
Survival Analysis
Technology Assessment
Telemedicine/Telehealth
Temporal Reasoning
Text Mining
Virtual Reality
Vocabulary and Terminology
Other

 
 



 
Online fulltext -oppikirjojen selaus:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books
 Vrt. ilmaiset klassikkokirjat:

http://www.gutenberg.org/


Artikkelien selaus:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
http://scholar.google.com/

http://www.terkko.helsinki.fi/journal/journal1.htm
http://www.bork.embl-heidelberg.de/xplormed/

"Gene Cards" (Vrt. jääkiekkokortit - Kerää koko sarja!)
http://bioinformatics.weizmann.ac.il/cards/
Biological text analysis:

  • AcroMed - A computer generated database of biomedical acronyms and the associated long forms extracted from the recent Medline abstracts
  • AbXtract - A prototype system for the automatic annotation of functional characteristics in protein families
  • MedMiner - Extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query
  • Protein Annotator's Assistant - A software system which assists protein annotators in the task of assigning functions to newly sequenced proteins
  • XplorMed
  • Lähtökohtia:
    http://www.ebi.ac.uk/services/index.html
    http://www.ncbi.nlm.nih.gov/
    http://www-db.embl-heidelberg.de/jss/SearchEMBL?compServ=x

    http://www.infobiogen.fr/services/deambulum/english/analyse.html

     
    Proteiinien sekvenssihaku:
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
    http://srs6.ebi.ac.uk/

     
    Blast-haku samannäköisille sekvenssin avulla:
    http://www.ncbi.nlm.nih.gov/BLAST/
     
     
    Suomalainen sekvenssien SRS-haku erityyppisistä tietokannoista:
    http://srs.csc.fi/srs/srs
     
    Haku parhaiten annotoidusta proteiinitietokannasta:
    http://us.expasy.org/sprot/
     
    Rakennekoordinaattien haku PDB:stä:
    http://www.rcsb.org/pdb/ 

    Patents
    http://fi.espacenet.com/                                                                                                                                                                                http://patents.uspto.gov/
    http://www.uspto.gov/patft/
    http://www.prh.fi/fi/patentit/linkkeja.html

    http://www.epoline.org/epoline/Epoline?language=EN&page=home&b=NS
     
    pFAM: (valmiiksi tehdyt multiple sequence alignmentit ym. msf-tiedosto sopii .txt:nä Courier New -fontilla talletettuna Clustaliin ladatuksi lähtökohdaksi dendrogrammien tekoon TreeViewssä)
    http://www.sanger.ac.uk/Software/Pfam/
     
    PUBCHEM
    http://pubchem.ncbi.nlm.nih.gov/
      

    SwissProt:
    http://au.expasy.org/sprot/
    http://www.isb-sib.ch/

    Proteomics tools:
    http://au.expasy.org/tools/
    http://us.expasy.org/sprot/
    sisältää mm.:
    Protein identification and characterization
    DNA -> Protein
    Similarity searches
    Pattern and profile searches
    Post-translational modification prediction
    Topology prediction
    Primary structure analysis
    Secondary structure prediction
    Tertiary structure
    Sequence alignment


    Uniprot
    http://www.ebi.uniprot.org/index.shtml
     
    Mallitusautomaatti:
    http://swissmodel.expasy.org//SWISS-MODEL.html
     
    DOMEENIARKKITEHTUURI:
    SMART, Simple Modular Architecture Research Tool
    http://smart.embl-heidelberg.de/ http://smart.EMBL-heidelberg.de/

    Downloads - Tietokannat PLUS ohjelmat (Clustal, Treeview etc.) serveriltä:
    http://bioweb.pasteur.fr/intro-uk.html

    Clustal X (etsi Googlella, vaihtuvat)
     Treeview (etsi Googlella, vaihtuvat)
     

    (Proteiinien yms.) visualisointiohjelmia
    Yksi ylitse muiden - PYMOL:                                                                                                                                                               http://pymol.sourceforge.net/                                                                                                                                               http://molvis.sdsc.edu/protexpl/frntdoor.htm
    http://www.umass.edu/microbio/rasmol/

    Dictionary/sanasto
    http://filebox.vt.edu/cals/cses/chagedor/glossary.html                                                                                                       http://www.csc.fi/molbio/sanasto/html/index.html                                                                                                                                                                    Muista myös Wikipedia ja Googlen Define-toiminto (Esim: Define:asperger)                                                                                                       

    Tärkeimpien molekyylibiologisten tietopankkien nykytilan katsaukset ilmestyvät perinteisesti NAR:n vuoden ensimmäisessä numerossa.
    Nucleic Acid Research  Esim.
    http://nar.oxfordjournals.org/content/vol33/suppl_2/index.dtl                                                                                           http://nar.oupjournals.org/content/vol31/issue1/


    Lipidomiikkaa:
    www.lipidmaps.org
    www.gerli.com
    www.genome-ad.jp/bride
    www.go.to/cyberlipid
    www.lipid.co.uk/infores/index.htm

     
    Glykomiikkaa:                                                                                                                                               http://www.functionalglycomics.org/static/consortium/

    Interaktiotietokantoja
    Database for Protein Interactions DPI:http://dip.doe-mbi.ucla.edu/
    Mammalian protein-protein interaction database (PPI):http://fantom21.gsc.riken.go.jp/PPI/
    Swissprot:http://www.expasy.ch/cgi-bin/keywlist.pl
    Molecular Interaction Database MINT: http://160.80.34.232/mint/index.html
    BIND: http://www.bind.ca/cgi-bin/bind/dataman
    Interdom: http://InterDom.lit.org.sg
    GRID: http://biodata.mshri.on.ca/grid/servlet/Index
    PIM: http://www.hybrigenics.fr/
    ProNet: http://pronet.doubletwist.com
    InterpreTS: http://www.russell.embl.de/interprets/
    STRING: http://www.bork.embl-heidelberg.de/STRING/
    ProDom:http://prodes.toulouse.inra.fr/prodom/
    Blocks: http://www.blocks.fhcrc.org/
    Pathcalling (yeast):
    http://portal.curagen.com/extpc/com.curagen.portal.servlet.Yeast
     

    Localization
    http://psort.ims.u-tokyo.ac.jp/

     
    Amigo:http://www.godatabase.org/cgi-bin/go.cgi
     
    Foldiklassifikaatiot ("Structural neighbors" PDB:n kautta)
    CATH:http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/CATHSrch.pl?query=1M4J&type=PDB
    CE: (http://cl.sdsc.edu/ce/all-to-all/all-to-all.html?1M4J)
    FATCAT: (http://fatcat.burnham.org/fatcat-cgi/cgi/struct_neibor/showChainNdomains.pl?pdbId=1M4J)
    FSSP: (http://columba.embl-ebi.ac.uk:8765/holm/qz?find=1M4J)
    SCOP: (http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.e.bhd.b.c.h.html)
    VAST: (www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?UID=1M4J )
     
    DALI
    http://www.ebi.ac.uk/dali/
     
    DNA-puoli:
    NCBI-sivusto (USA:n)
    EMBL tai EBI -sivusto (EU:n)
    MapViewer:
    http://www.ncbi.nlm.nih.gov/mapview/
    http://www.firstmarket.com/firstmarket/cutter/

    http://biocenter.helsinki.fi/bi/rnd/biocomp/prog2.html


    Introneita
    http://www.cbs.dtu.dk/services/NetPGene/


    Promoottorianalyysiä:
    MEME
    http://meme.sdsc.edu/meme/website/meme.html

    TFSCAN
    http://bioweb.pasteur.fr/seqanal/interfaces/tfscan.html

    POBO
    http://ekhidna.biocenter.helsinki.fi:9801/pobo/index_html

    MATCH e0d7c2eb
    http://www.gene-regulation.com/pub/programs.html#match

    Kaupallisen lisenssin vaativa TRANSFAC
    http://www.gene-regulation.com/pub/databases.html

     

    Solun signaalinvälityskarttoja & metaboliakarttoja:                                                                                                                                      http://www.biocarta.com/                                                                                                                                                                                    Signaalinvälitysreitit integroituina: Löytyy On-line tutorial
    http://www.biobase.de/pages/products/databases.html
    Microarrays: Ekspressiotietokanta (geenien ilmentäminen mRNA-tasolla)
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds                                                                                                                       http://www.ebi.ac.uk/arrayexpress/
    http://genome-www5.stanford.edu/MicroArray/SMD/

    Biological Search Engines/biologian hakurobotteja                                                                                                                   http://www.r9corporation.fsnet.co.uk/
    http://www.biolinks.net.ru/Search_Engines/    

    Protokollia/reseptejä/keittokirjoja labraan:
    http://www.bioinformatics.vg/biolinks/bioinformatics/Tutorials.shtml                                                           http://www.fhcrc.org/labs/hahn/methods/methods_index.html
    http://news.bmn.com/hmsbeagle/
    http://www.horizonpress.com/gateway/protocols.html#dab
    http://www.cellbio.com/protocols.html

    (Enemmän solubiologiaa kuin kemiaa.)
    http://www.leeds.ac.uk/bionet/compend/contents.htm
    Solubility calculator for molecules: http://www.logp.com/
    Buffer calculators:
    http://www.nottingham.ac.uk/~mbzspd/HHCalc.html
    http://www.bi.umist.ac.uk/users/mjfrbn/buffers/makebuf.asp
    http://researchlink.labvelocity.com/tools/bufferCalculator.jhtml

    m=cVM                                                                                                                                                                                                                    c1V1=c2V2

    Professori Vihisen vihikoirat ja -serverit:
    http://bioinf.uta.fi/
    (Mene keskeltä vasemmalta database linkkeihin)

    Muuta luentomateriaalia/oppaita linkkeineen:

    http://www.bioinformatics.vg/biolinks/bioinformatics/Tutorials.shtml
    http://www.bioinformatics.vg/biolinks/bioinformatics/Training%2520and%2520Education.shtml   http://staff.cs.utu.fi/kurssit/johdatus_bioinformatiikkaan_I/syksy_2002/luento4.pdf
    http://saato014.hut.fi/Hyotyniemi/Publications/2001_arpakannus/GromovUusi.pdf
    http://compbio.uchsc.edu/Hunter_lab/Hunter/pharm-postdocs-01.ppt

    jne. jne.
    Step-by-step on-line oppaita ohjattuine mallihakuineen:
    http://www.ncbi.nlm.nih.gov/Education/
    http://www.ncbi.nlm.nih.gov/About/primer/

    http://bioinformatics.weizmann.ac.il/hotmolecbase/webscience.htm                                                                                                                                            Laajat linkkilistat:
    http://us.expasy.org/alinks.html
    http://users.evitech.fi/~henriva/Bookmark.htm
    http://www.public.iastate.edu/~pedro/research_tools.html
    http://mcb.harvard.edu/BioLinks.html
    http://www.yk.rim.or.jp/%7Eaisoai/link.html
    http://www.up.univ-mrs.fr/~wabim/english/logligne.html
    Plasman 2D geelit
    http://www.expasy.org/cgi-bin/show_thumbnails.pl
    http://www-lmmb.ncifcrf.gov/2dwgDB/2DWG.html
    http://us.expasy.org/ch2d/ch2d-top.html
    http://www-lecb.ncifcrf.gov/cgi-bin/dbEngine/2dwgDB,getTableDataByID,plasma
    http://us.expasy.org/cgi-bin/get-ch2d-table.pl
    http://www-lecb.ncifcrf.gov/flicker/f2plasmaLbl.html
    http://www-lecb.ncifcrf.gov/EP/table2Ddatabases.html
    http://www-lmmb.ncifcrf.gov/plasmaDB/plasmaL.html
    http://www-lmmb.ncifcrf.gov/plasmaDB/plasmaH.html
    http://www-lecb.ncifcrf.gov/NCISEM97/ncisem-plasmaMap.html
    http://www-lecb.ncifcrf.gov/ABRF97/abrf4.html
       


    CSC:n Bio-opas (vanha)
    http://www.csc.fi/oppaat/bio/

    Rekisteritutkimus suomalaisista virastoista:
    http://www.duodecim.fi/kotisivut/kotisivut.sivut.nayta?p_sivu=22970
     
    EMBOSS
    http://www.emboss.org
     
    Genomes
    http://www.ncbi.nlm.nih.gov/Entrez/Genome/main_genomes.html                                                                               http://www.nature.com/genomics/papers/index.html
    TreeBASE:http://herbaria.harvard.edu/treebase


    Amino Acid nomenclature & structures:
    http://www.indstate.edu/thcme/mwking/amino-acids.html
    http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/aa.htm
    http://wbiomed.curtin.edu.au/teach/biochem/tutorials/AAs/AA.html
    http://www.nidlink.com/~jfromm/chem301/chem302r.htm

    (Enzyme nomenclature & classification)
    http://us.expasy.org/enzyme/
    Metabolical pathways
    http://www.expasy.org/cgi-bin/show_thumbnails.pl
    Pathways: cellular and molecular processes
    http://www.expasy.org/cgi-bin/show_thumbnails.pl?2
    3D -rakenteiden tietokanta: PDB=Protein Data Bank
    http://www.rcsb.org/pdb/



    Kuriositeetteja, extraa:
    HapMap:                                                                                                                                                                               http://www.hapmap.org/index.html.en

    SNP consortium:
    http://snp.cshl.org
    http://recode.genetics.utah.edu/cgi-bin/WebObjects/RecodeWeb.woa

    (Programmed ribosomal frameshifting, codon redefinition and translational bypass)
    ASAP: Alternative splicing annotation project
    http://www.bioinformatics.ucla.edu/ASAP
    BSD: Biodegradative Strain Database
    http://bsd.cme.msu.edu                                                                                                                                                                                                        BRITE:http://www.genome.ad.jp/brite/
    MIPS: http://mips.gsf.de/
    ASAP: A Systemic Annotation Package for Community Analysis of Genomes:
    Htpps://asap.ahabs.wisc.edu/annotation/phb/ASAP1.htm


    Fun:
    http://www.xs4all.nl/~jcdverha/scijokes/               http://www.improb.com/                                                                                                                                                                                   http://au.expasy.org/cgi-bin/sw-jokes.pl                                                                                                                                       http://cagle.msnbc.com/news/gene/gene2.asp                                                                                                                           http://www.almaz.com/nobel/nobel.html
    http://www.improbable.com/ig/igtop.html                                                                                                                                                                                                                                                                                                                                                                           

                                                                   

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