Technology Resources

This page provides links to helpful web resources.

Bioinformatics Resources

Data, schemas and resources for bioinformatics
    Metadata Standards
  • Dublin Core Terms Information science metadata standards.
  • Darwin Core Terms Biodiversity metadata standards.
  • PaleoCore Terms Paleontology metadata standards.
  • CIDOC-crm Standards and ontologies for cultural heritage management.

  • Biodiversity
  • GBIF the Global Biodiversity Information Facility. Making biodiversity data available on the net.
  • VertNetBiodiversity Database. A combined data portal for the FishNet, MaNIS, HerpNET, ORNIS databases.
  • IDigBio Museum collections database portal.
  • Global Mammal Parasite Database a comprehensive collection of host-parasite records from the published scientific literature and supplemented with original data on taxonomy, sampling localities, and parasite characteristics, such as transmission mode. The data can be used to investigate mammalian socioecology, parasite "spillover" to humans, and human evolution.

  • Paleontology
  • ETE database the Evolution of Terrestrial Ecosystems database at the Smithsonian.
  • Paleobiology Datase a comprehensive database of paleontological occurrences, as reported in the paleontological literature.
  • NOW database the New and Old World fossil mammal database

  • Paleoanthropology
  • PaleoCore Data repository for paleoanthropology.
  • eFossils Fossil sites and specimens.
  • eLucy online guide to the famous Lucy fossil from Hadar.
  • CASHP Human Origins Database A paleoanthropology database.
  • RHOI specimen database the database for the Revealing Hominid Origins Initiative.
  • PRIMO the NYCEP PRImate Morphometrics Online database, is an open-access resource for a range of data types. Caliper data on teeth and skulls of cercopithecids (and a few hominoids) are posted now, and 3D Microscribe digitizer landmark data are being prepared for inclusion. Surface scans (as well as digital images) will be available later, as will additional geographical information.
  • PaleoanthPortal provides links to active databases in paleoanthropology. The plan is for it to serve as a portal through which users may search such databases from a single entry point without visiting their sites directly; this may direct users to those databases which contain information of the type sought and avoid those which don't.
  • NESPOS Pleistocene people and places.
  • Fossilized.org Database of Paleoanthropology sites
  • Catalogue of Fossil Hominids Database

  • Archaeology
  • Open Context Data repository for archaeology, specializing in Europe and the Middle East.
  • tDAR the Digiral Archaeological Record.
  • OCHRE Online Cultural and Historical Research Environment. A data management service for classical archaeology.
  • Stage Three Archaeology Database at Cambridge University of Earth Sciences
  • Fossilized.org Database of Paleoanthropology sites

  • Image and Morphology
  • eSkeletons online comparative osteology.
  • DigiMorph repository of 3D and CT scan data.
  • Morphobank an online workspace for phylogenetic research on phenotypes (e.g., morphology, behavior, development). A web application and database, it has a user-friendly interface for collaboration on phylogenetic matrices in real time in a private workspace, and intuitive media tools.
  • Morphobrowser a 3D digitial specimen database.
  • Morphosource a 3D digitial specimen database.
  • ESRF Virtual Database a digitial specimen database for the European Synchrotron Radiation Facility.

  • Geology and Chronology
  • PeriodO Time periods Organized.
  • Chronos Geochronology working group.

  • Taxonomy and Systematics
  • DELTA DEscription Language for TAxonomy. One of the first computer implimentations of a taxonomic system.
  • Nomenclator Zoologicus a comprehensive database of taxonomic Genera since Linnaeus.
  • Encyclopedia of Life Global access to knowledge about life on earth.

  • General
  • Dryad an online repository for published datasets in the basic and applied biosciences.

Programming Resources

Computer programming languages, IDEs, libraries
  • Python An elegant language and perfect for acdademic programming
  • R A not-so-elegant but very powerful statistical programming language. Excellent for ecology and paleobiology.
  • R Studio An excellent cross platform IDE for R
  • Tinn-R A Windows based editor and IDE for R. For you poor souls who don't (yet) have macs.
  • ggplot2 Hadley Wickham's grammar of graphics. The best way to make plots in R. See also Andrew Barr's basic introduction to using ggplot2.
  • reshape Another great R package from Hadley Wickham for structuring data.
  • RPy A simple, yet robust, python interface to the R programming language. Two great tastes that taste great together.
  • Julia A high level programming language similar to python, perl and java.
  • Eclipse Cross-platform programming IDE for Java, C++, and Python (with PyDev)
  • PyDev A plugin to Eclipse that provides functionality for Python and Jython programming.
  • Boa Constructor Cross-platform IDE and GUI development for Python.
  • Xcode Apple's excellent IDE and GUI development platform. Now supports python via PyObjC.
  • Jython A wrapper for Python in Java
  • REALBasic If you simply must use basic. Nice GUI development and DB integration.
  • Python vs. Java? Comparison between the two languages.
  • TeXshop Typsetting for the fierce.
  • LyX The only way to LaTeX! A great open source document processor. What you see is what you mean
  • Sweave Embed R in your Lyx documents. That's right, dynamic document production with embedded R code!
  • Reproducible Research A new approach to scientific publishing.
  • JabRef Cross-platform bibtex database management tool.
  • LaTeX bibliography database A database of LaTeX bibliographic styles for different journals.
  • fink Open source package management tool for mac.
  • gentoo Brass knuckles linux distro for those who like to customize...everything! Great documentation and online support.
  • ubunto User friendly linux distro for those who don't need an extra headache.
  • Red Hat Tried and true enterprise ready linux distro.

Web Resources

HTML editors, Web Application Servers
  • Taco A nice, lightweight HTML editor for Mac.
  • Django Pythonic web application framework. Fantastic.

Database Resources

Database management systems, DB clients
  • SQLite An open-source, light-weight, cross platform database engine
  • SpatiaLite A spatially aware open-source database engine.
  • PostgreSQL An open source relational database management system (RDBMS) that is geospatially enabled.
  • PostGIS PostGIS adds support for geographic objects to the PostgreSQL object-relational database.The stuff that makes PostgreSQL geospatially enabled.
  • XMLSpy A windows based XML editor
  • oXygen A mac based XML editor
  • DBVisualizer Cross-platform database administration and editing tool.
  • Database Spy Windows based database administration and editing tool. From the makers of XML Spy.