Molecular Databases

Organismal Databases

Organismal Databases
  • International Working Group on Taxonomic Databases. International Union of Biological Sciences.
  • TreeBASE. A database of phylogenetic trees and data matrices published in the primary systematic literature.
  • Cladestore. An electronic source of data matrices from published cladograms. University of Bristol.
  • Species 2000. An effort to index the world’s known species.
  • BIOSIS. The world’s largest collection of abstracts and bibliographic references to worldwide biological and medical literature.
  • Integrated Taxonomic Information System (ITIS). On-line list of biological names focusing on the biota of North America.
  • National Biological Information Infrastructure (NBII). An electronic gateway to biological data and information maintained by federal, state, and local government agencies, private sector organizations, and other partners around the nation and the world.
  • TimeTree. A database of species divergence times. Penn State and Arizona State University.
  • WildFinder. Mapping the World’s Species. A map-driven, searchable database of more than 30,000 bird, mammal, reptile, and amphibian species worldwide. World Wildlife Fund.
  • Global Invasive Species Database. IUCN/SSC Invasive Species Specialist Group (ISSG).
  • uBio – Universal Biological Indexer and Organizer. A system of client and server tools that interact with the Taxonomic Name Server (TNS), which serves authoritative taxonomic opinions within a multi-classification framework. The Marine Biological Laboratory, Woods Hole.
  • OBIS.   Ocean Biogeographic Information System. A globally-distributed network of systematic, ecological, and environmental information systems to communicate biological information about the ocean.
  • World Data Centre for Microorganisms. Provides a comprehensive directory of culture collections, databases on microbes and cell lines.
  • InfoNatura. Birds and mammals of Latin America. Association for Biodiversity Information in collaboration with the Natural Heritage Network.
  • Fauna Europaea. A database of all European land and fresh-water animals.
  • Kingdoms Project’s Natural Sciences Databases. Collaborative project of the Illinois State Academy of Science, the Illinois State Museum, and the Weizmann Institute of Science.
  • Man and the Biosphere Species Databases. Databases of vascular plant and vertebrate animal occurrences on the world’s biosphere reserves and other protected areas.
  • Species in Parks: Flora and Fauna Databases. Databases of vascular plant and vertebrate animal species reported to occur within lands managed by the U.S. National Park Service.
  • Threatened Animals of the World. A database maintained by the World Conservation Monitoring Centre.
  • Base de Dados Tropical (BDT). Tropical Data Base of the André Tasello Foundation, Brazil. A variety of databases providing biological information of environmental and industrial interest.
  • Biota of North America Program (BONAP). Data for all vascular plants and vertebrate species (native, naturalized, and adventive) of North America, north of Mexico.
  • MaPSTeDI. A collaborative effort between the University of Colorado Museum, Denver Museum of Nature and Science, and Denver Botanic Gardens to convert separate collections into one distributed biodiversity database and research toolkit for the southern and central Rockies and adjacent plains.
  • German Collection of Microorganisms and Cell Cultures (DSMZ). An independent, non-profit organization dedicated to the acquisition, characterization and identification, preservation and distribution of Bacteria, Archaea, fungi, plasmids, phages, human and animal cell lines, plant cell cultures and plant viruses.
  • The Fossil Record 2. A near-complete listing of the diversity of life through time, compiled at the level of the family. University of Bristol.
  • The Paleobiology Database. Providing global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age.
  • PaleoBank. A relational database for invertebrate paleontology.
  • NMITA: Neogene Marine Biota of Tropical America . An online biotic database containing images and data for taxa used in analyses of Tropical American biodiversity over the past 25 million years.
  • PaleoBase. An illustrated, relational database of invertebrate fossils for education and research. The Natural History Museum, London.
  • Brain Biodiversity Bank. National Museum of Health and Medicine, Michigan State University, University of Wisconsin.

Catalogue of Life

Found a website that lets you drill down from Kingdom all the way to species called the Catalogue Of Life:



King Phillip Cried Out For Good Soup

At least that is memory aide that I learned in high school to remember the different layers of biological taxonomy.


Each species is grouped into genus by a common traits.  The genus are group into family.  Family into Order.  Order into Class.  Class into Phylum.  And finally Phylum into Kingdom.  There are different number of kingdoms depending on who you talk to, how they define life, and when they learned taxonomy.  Let’s look at six of them.

Archaebacteria, Eubacteria, Protista, Fungi, Plantae, Animalia

We humans are under the Animalia Kingdom.  Here is how it maps out for us:

Domain Eukarya

  • Kingdom Animalia
  • Phylum Chordata
  • Subphylum Vertebrata
  • Class Mammalia
  • Order Primates
  • Family Hominidae
  • Genus Homo
  • Species sapiens

What I am looking for is a website that will let me click on Animalia, and see the different Phylums.

I found a highly scientific tool at the NCBI called Taxonomy Browser.   But it only includes single celled lifeforms.  And it is targeted at the specialist.

Any ideas?



Mars One – More Reality TV and Less Real

Have you heard about Mars One?  Here is what they say they are:

Mars One is a private, apolitical organization whose intent is to establish a colony on Mars through the integration of existing, readily available technologies from industry leaders world-wide. Unique in its approach, Mars One intends to fund this decade-long endeavor through an interactive, reality TV style broadcast from astronaut selection to robotic construction of the outpost; from the seven month flight through the first years on Mars.

Now, I love the idea of going to Mars.  I am OK even with having one way trips to do so.  (Got to die somewhere, right?)  I really love the video they put together:

And I would love to believe that they would be able to pull it off.  But they do not have the funds or the staff to pull it off.  They do not have the billions that would be required or the expertise.

Here is the timeline that they currently plan:


This will be the year in which our astronaut selection begins! Who will be the first four humans on Mars and who are to follow every two years after? Anyone who meets the criteria and feels they are up to the challenge can apply. Mars One will maintain 40 trained astronauts during the full duration of its missions.

By the close of 2013, Mars One will build a replica of the Mars settlement on Earth, likely in a cold, desolate environment, to help the astronauts prepare and train and for a realistic environment in which to test the equipment. The astronaut selection and the preparations in the simulated Mars base will be broadcast world-wide for the public to view.


The supply mission will be launched for Mars in January 2016. It will land on the Red Planet in October 2016 with its cargo of 2500 kilograms of spare parts, solar photovoltaic panels, and general supplies. It will land close to where the outpost is expected to be.


What will most definitely happen is that in 2013 a call will be put out for volunteers wanting to go to Mars.  There really will be training and a mock up built here on earth.  It really will be a media spectacle.  There will be sponsors for the show.  And it will make considerable amount of money.  Probably in the $100 of millions.

What will not happen is actually sending anything into space.  The entire event will be done here on the grown, with no hope of anything be launched into orbit.  There will especially not be anything or anyone going to Mars because of this.

Why?  Well you see, the ground stuff is safe and cheap.  It also makes for better TV.  But anything that is actually sending things to space is costly, risky, and does not make for good TV.  It won’t happen being funded this way, with this group of people.

I wish it were otherwise.  And I hope I am wrong.  But I do not see how I could be…

Getting Started with Processing

What is Processing?

Processing is a computer language.  It can be downloaded at  It’s creators confess:

Processing seeks to ruin the careers of talented designers by tempting them away from their usual tools and into the world of programming and computation. Similarly, the project is designed to turn engineers and computer scientists to less gainful employment as artists and designers.

It is uses a similar IDE as Arduino.  And many people use Processing and Arduino together.  Processing runs on the computer and can interact with the arduino over the serial port allowing for you to create a bridge between the desktop/online world and your handcrafted/custom electronic devices.

What can you do with Processing?

Ok, interested enough to get this far?  Take a look at these examples:

How to learn Processing?

First you will need to install it:

Then I recommend going through this online tutorial:

If you are using Processing, leave a comment.