Research tools

Making information accessible to all is one of the main duties of scientists. New technology has made this more possible: rather than being confined to taxonomic works with limited distribution, keys can be placed online; rather than witholding information about new primers and protocols until the paper that uses them is published in months or years, this information can be released as it is generated, helping all. One barrier to this is technological: relational databases, for example, can be tremendously helpful for keeping projects organized and distributing information, but require a bit of effort to learn how to use. This website has some examples and instructions based on what I have cobbled up while working on my project on Myrmecocystus ants. I've found these tools useful, but as I'm still a bit of a neophyte, there are undoubtably ways to improve them. This page still under construction.

Online key: Describes how to implement a dichotomous key online using a MySQL database and perl cgi scripts. This site, as do all the ones here, includes sample code and detailed instructions, so do not fear if you do not yet know what MySQL or perl cgi scripts are.

Species pages: Each species in my project has a page that is dynamically generated, containing information about that species from the web (such as whether it has sequences in Genbank) and from my work (it uses my project database to report which primers and PCR programs have been successful).

Project database: I use a relational database to keep track of collected specimens, DNA extractions, PCRs, sequencing reactions and results, morphological measurements, etc. A perl script is used to interact with this database. This combination greatly streamlines my work: for a given set of PCRs that need to be sequenced, for example, the program generates a lab notebook page that lists all the reagents needed, taking into account the concentration of each PCR sample and varying needs to dilute each sample. Once DNA sequences are returned from our sequencing facility, the program records the sequence quality in the database and converts the sequence file names to more useful ones.


		Research tools How to make online keys, manage a collection and sequencing project using perl and MySQL, generate dynamic species pages, etc.

		Making information accessible to all is one of the main duties of scientists. New technology has made this more possible: rather than being confined to taxonomic works with limited distribution, keys can be placed online; rather than witholding information about new primers and protocols until the paper that uses them is published in months or years, this information can be released as it is generated, helping all. One barrier to this is technological: relational databases, for example, can be tremendously helpful for keeping projects organized and distributing information, but require a bit of effort to learn how to use. This website has some examples and instructions based on what I have cobbled up while working on my project on Myrmecocystus ants. I've found these tools useful, but as I'm still a bit of a neophyte, there are undoubtably ways to improve them. This page still under construction. Online key: Describes how to implement a dichotomous key online using a MySQL database and perl cgi scripts. This site, as do all the ones here, includes sample code and detailed instructions, so do not fear if you do not yet know what MySQL or perl cgi scripts are. Species pages: Each species in my project has a page that is dynamically generated, containing information about that species from the web (such as whether it has sequences in Genbank) and from my work (it uses my project database to report which primers and PCR programs have been successful). Project database: I use a relational database to keep track of collected specimens, DNA extractions, PCRs, sequencing reactions and results, morphological measurements, etc. A perl script is used to interact with this database. This combination greatly streamlines my work: for a given set of PCRs that need to be sequenced, for example, the program generates a lab notebook page that lists all the reagents needed, taking into account the concentration of each PCR sample and varying needs to dilute each sample. Once DNA sequences are returned from our sequencing facility, the program records the sequence quality in the database and converts the sequence file names to more useful ones. Site map/search Page hits: