Bio-Tools

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Bio Tools
Welcome to Bio-Tools. The internet is a vast wasteland of links and tubes. I'm a tube-dweller who hoards links to interesting and useful places. Go now, and explore my eclectic collection of utensils continuously updating for your fecundity.
Last Updated: Sep. 4 2021
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  [ {"heading":"Taxonomy"
    ,"links":
      [["Lifemap (My favorite)","http://lifemap-ncbi.univ-lyon1.fr"]
      ,["OneZoom Explorer","http://www.onezoom.org"]
      ,["One Tree of Life","https://tree.opentreeoflife.org"]
      ,["Bacteria Tree of Life","http://annotree.uwaterloo.ca/app"]
      ,["Interactive Tree of Life","https://itol.embl.de/itol.cgi"]
      ,["FoamTree of Life","https://get.carrotsearch.com/foamtree/latest/demos/large.html"]
      ,["Eukaryotic ToL","https://eukmap.unieuk.org"]
      ]
    }
  , {"heading":"Organism Identification"
    ,"links":
      [["Discover Life","https://www.discoverlife.org"]
      ,["iNaturalist","https://www.inaturalist.org/observations?place_id=any&subview=map"]
      ,["Zooplankton Key","http://cfb.unh.edu/cfbkey/html/groups.html"]
      ,["PhycoKey (Algae)","http://www.cfb.unh.edu/phycokey/phycokey.htm"]
      ,["MycoKey (Fungi)","http://www.mycokey.com/newMycoKeySite/MycoKeyIdentQuick.html"]
      ,["Insect Identification","https://www.insectidentification.org"]
      ,["Marine Species Identification","http://species-identification.org"]
      ,["(Pl@ntNet) AI Plant Identification","https://identify.plantnet.org"]
      ,["Featured Creatures","http://entnemdept.ufl.edu/creatures"]
      ,["Slime Mold (Eumycetozoans)","http://slimemold.uark.edu"]
      ,["Phone Apps","https://www.tristanhenderson.info/education/identifyapps"]
      ]
    }
  , {"heading":"Biodiversity"
    ,"links":
      [["Encyclopedia of Life","https://eol.org"]
      ,["Integrated Taxonomic Information System","https://www.itis.gov"]
      ,["World Register of Marine Species (WoRMS)","http://www.marinespecies.org/"]
      ,["Ocean Biodiversity Information System (OBIS)","https://obis.org"]
      ,["Global Biodiversity Information Facility","https://www.gbif.org"]
      ,["ViralZone","https://viralzone.expasy.org/"]
      ,["Phytoplankton Encyclopedia","https://www.eoas.ubc.ca/research/phytoplankton/"]
      ,["EBI Microbiome Initiative","https://www.ebi.ac.uk/metagenomics"]
      ,["World of amoeboid organisms","https://www.arcella.nl/introduction"]
      ,["Penard Labs (amoebae)","http://www.penard.de/Tidbits/#-1"]
      ,["DiatomBase","https://www.diatombase.org/index.php"]
      ,["Mycobank","https://www.mycobank.org"]
      ,["AlgaeBase","https://www.algaebase.org/"]
      ]
    }
  , {"heading":"Paleobiology (fossils and more)"
    ,"links":
      [["Smithsonian Collections","https://collections.nmnh.si.edu/search"]
      ,["AMNH Databases","https://www.amnh.org/research"]
      ,["AMNH Library","https://digitallibrary.amnh.org"]
      ,["Morphobank","https://morphobank.org"]
      ,["Microfossil Collection","https://www.ucl.ac.uk/GeolSci/micropal"]
      ,["Biodiversity Heritage Library","https://www.biodiversitylibrary.org"]
      ,["Yale Peabody Museum Collections","https://collections.peabody.yale.edu/search/"]
      ]
    }
  , {"heading":"Paleo-Earth and Maps"
    ,"links":
      [["GPlates Portal","http://portal.gplates.org"]
      ,["Google Earth","https://earth.google.com/web"]
      ,["Platetectonic Reconstruction","https://www.odsn.de/odsn/services/paleomap/paleomap.html"]
      ,["Scotese Climate History","http://www.scotese.com/climate.htm"]
      ,["GPlates, 3D Earth Modelling Software","http://www.lighthouse3d.com/tutorials/maths/ray-triangle-intersection/"]
      ,["EarthByte, Virtual Earth Tools","https://www.earthbyte.org/"]
      ,["Scotese PaleoAtlas Data","https://www.earthbyte.org/paleomap-paleoatlas-for-gplates"]
      ,["PBDB Navigator, Fossil Locations in Space/Time","https://paleobiodb.org/navigator"]
      ,["Old Maps Online","https://www.oldmapsonline.org"]
      ]
    }
    , {"heading":"Earth, Ecosystem, and Ocean Tools"
    ,"links":
      [["CEC Atlas","http://www.cec.org/files/atlas/?z=3&x=-93.1641&y=61.9803&lang=en&layers=polbounds%2Clandcover2015ls&opacities=100%2C100&labels=false"]
      ,["USGS Water Resources","https://www.usgs.gov/mission-areas/water-resources/maps"]
      ,["USGS Mineral Resources","https://www.usgs.gov/energy-and-minerals/mineral-resources-program/maps"]
      ,["NOAA Ocean Data","https://www.ndbc.noaa.gov"]
      ,["NOAA Tides and Currents","https://tidesandcurrents.noaa.gov"]
      ,["Plantmaps","https://www.plantmaps.com/index.php"]
      ,["North American Pollution Registry","http://takingstock.cec.org/map"]
      ,["Global Biotic Interactions","https://www.globalbioticinteractions.org/"]
      ,["Texas Ecosystem Mapper","https://tpwd.texas.gov/gis/team/"]
      ,["EPA State Ecoregions Data","https://www.epa.gov/eco-research/ecoregions"]
      ,["Snow and Ice Data Center","https://nsidc.org/data"]
      ,["37 Year Earth Timelapses","https://earthengine.google.com/timelapse/"]
      ,["Earth Engine Datasets","https://developers.google.com/earth-engine/datasets/"]
      
      ]
    }
    , {"heading":"Microscopy and Histology"
    ,"links":
      [["Microscopy University","https://www.microscopyu.com/"]
      ,["Brain Map","https://portal.brain-map.org/"]
      ,["ImageJ (software)","https://imagej.net/Welcome"]
      ,["Micrographia","https://www.micrographia.com/index.htm"]
      ,["PSmicrographs","https://psmicrographs.com/"]
      ,["Microscopy UK","http://www.microscopy-uk.org.uk/"]
      ,["Zeiss Microscopy Education","http://zeiss-campus.magnet.fsu.edu/"]
      
      ]
    }
    , {"heading":"General Databases"
    ,"links":
      [["Wolfram Alpha (everything)","https://www.wolframalpha.com/"]
      ,["Manual Search Engine for Equipment","https://www.manualslib.com/"]
      
      ]
    }
    , {"heading":"Molecular, Biochemistry (Proteins), Organics"
    ,"links":
      [["NCBI Resources","https://www.ncbi.nlm.nih.gov/guide/all/"]
      ,["UniProt (proteins)","https://www.uniprot.org/"]
      ,["Protein Data Bank","https://www.rcsb.org/"]
      ,["AlphaFold Structure Prediction","https://alphafold.ebi.ac.uk/"]
      ,["I-TASSER Protein Structure Prediction","https://zhanglab.ccmb.med.umich.edu/I-TASSER/"]
      ,["Human Protein Atlas","https://www.proteinatlas.org/"]
      ,["Biochemical Pathways Map","http://biochemical-pathways.com/#/map/1"]
      ,["Extracellular Matrix Interaction Database","http://matrixdb.univ-lyon1.fr/"]
      ,["Reactome Pathway Browser","https://reactome.org/"]
      ,["Spectral Database (Organic)","https://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"]
      ,["Infrared Spectroscopy Table","https://en.wikipedia.org/wiki/Infrared_spectroscopy_correlation_table"]
      ,["Fluorescent Protein Database","https://www.fpbase.org/"]
      
      ]
    }
    , {"heading":"Bioinformatics and Working with DNA"
    ,"links":
      [["Swiss Bioinformatics Resource Portal","https://www.expasy.org/"]
      ,["UCSC Genome Browser","https://genome.ucsc.edu/"]
      ,["Benchling (DNA Platform)","https://www.benchling.com/"]
      ,["Zhang Lab Tools","https://zhanglab.ccmb.med.umich.edu/"]
      ,["MicroRNA Database","http://www.mirbase.org/"]
      ,["NEB Cloning Tools","https://www.neb.com/tools-and-resources/interactive-tools"]
      ,["Natural Product Domain Seeker","https://npdomainseeker.sdsc.edu/napdos_home.html"]
      ,["Galaxy Bioinformatics Platform","https://usegalaxy.org/"]
      ,["Ribosomal Database Project","https://rdp.cme.msu.edu/index.jsp"]
      ,["bio.tools (tons of bio-inf tools)","https://bio.tools/"]
      ]
    }
    , {"heading":"Organismal Genome Databases"
    ,"links":
      [["DictyExpress (Slime mold)","https://dictyexpress.research.bcm.edu/landing"]
      ,["Ciliates","http://ciliates.org/index.php/home/welcome/"]
      ,["EukRef Eukaroytic Environmental Sequencing","https://pr2-database.org/eukref/about/"]
      ]
    }
    , {"heading":"Chemistry and Particles"
    ,"links":
      [["PubChem","https://pubchem.ncbi.nlm.nih.gov/"]
      ,["(The best) Periodic Table","https://ptable.com"]
      ,["Nuclear Data Center (KAERI)","http://atom.kaeri.re.kr/"]
      ]
    }
    , {"heading":"Scientific Illustration"
    ,"links":
      [["BioRender","https://biorender.com/"]
      ,["The Noun Project (Icons)","https://thenounproject.com/"]
      ,["SciDraw","https://scidraw.io/"]
      ,["Cell Illustrator","http://www.cellillustrator.com/"]
      ,["CellDesigner","http://www.celldesigner.org/"]
      ]
    }
    , {"heading":"Free Articles and Textbooks (Disclaimer: use at your own risk.)"
    ,"links":
      [["Sci-Hub Pub","https://www.sci-hub.pub/"]
      ,["Sci-Hub Backup","https://libgen.ggfwzs.net/"]
      ,["Library Genesis","http://libgen.rs/"]
      ,["Z-Library","https://1lib.us/"]
      ,["Book Search Engine (Sketchy)","https://cse.google.com/cse?cx=011394183039475424659:5bfyqg89ers"]
      ,["Penguin Papers (Very Sketchy)","https://doi.qqsci.com/"]
      ]
    }
    , {"heading":"Unique Spaces to Buy Equipment and More"
    ,"links":
    [["Government Surplus","https://www.govdeals.com/"]
    ,["Microscopy Supplies and More","https://www.emsdiasum.com/microscopy/products/catalog.aspx"]
    ,["Rare Botanical and Antique Prints","http://www.panteek.com/"]
    
    ]
  }
  , {"heading":"Other Link Hubs, Portals, and People (meta)"
  ,"links":
  [["Slime Mold Portal","http://slimemold.uark.edu/links.htm"]
  ,["Ferry Siemensma Collection","https://www.arcella.nl/useful-links"]
  ,["3D Print Labware","https://open-labware.net/links-2/"]
  
  ]
}
, {"heading":"Academics"
,"links":
[["Academics Family Tree","https://academictree.org/"]

]
}
  
  ]