The Present

• Institute for Systems Biology:

  [ RoR, Solr ]

• At the Institute for Systems Biology (ISB) I am working on a project that will provide an archiving system for experiments. The experiments are entered into the system along with descriptive information (metadata). Being able to search for the experiments via metadata will generate lists of related experiments to show what has already been tested. This will aid in minimizing duplication of expensive experiments as well as provide a means for exporting a selected experiment's raw data to be processed further by exporting the raw data to the users analysis application of choice.

The Past

• UW College of Engineering:

  [ PHP, Drupal ]

• At the University of Washington's College of Engineering (CoE), I created, updated and maintained web applications that helped faculty, staff and students perform processes and procedures in an online format. Whether it was an application for applying to the College, applying for a scholarship or searching for faculty members, I was a part of creating the online experience.


• In 2007 the College decided to redesign their website to become more aligned with the main University of Washington brand. I was involved in the site redesign process as well as getting the site up and running in the Drupal CMS. I was responsible for modifying and maintaining the Drupal installations for the CoE site and the HCDE site.


• Geospiza Inc.:

  [ Perl/BioPerl ]



• There was a need to add more functionality to Geospiza's DNA sequence analysis software. I created a protein translation feature to their software suite that allows a scientist to easily view the 6 protein translations DNA sequence (3 Forward, 3 Reverse). Due to proprietary information I am not able to show code, but I have provided a partial screenshot of the final product.


• Broad Institute:

  [ Perl, Java ]

• I assisted with the design and development of a software application that searches DNA sequences from an isolated human population for new alleles of Streptococcus pneumoniae. Once the new alleles are found they are uploaded to a public database. Many scientists from around the world use the data in their research.


• The Special Projects team needed a way to track their DNA samples outside of the main production pipeline system. I assisted with the design and development of a smaller, specialized sample tracking system that allowed the special projects team to have finer control over unique (one-off) samples.


• I created a Java application that would read in DNA sequencing files generated by an ABI 3730xl instrument used for sequencing DNA. A user would choose the folder in which the files existed and then click the "generate graph" button. A graph showing the average phred20s for the sequencing run would be displayed. Evaluating the average phred20s for a sequencing run this way was used to determine the quality of the 100+ sequencing instruments used in production.

Contact:

Email: kmfoley [at] kmfoley [dot] com