Difference between revisions of "Template:Research completed"

Revision as of 17:55, 10 October 2017

• September 2015 – present: Cloud Engineer at Redapt, Seattle, USA.

Skills used: Linux, OpenStack, AWS, Docker, etcd, Kubernetes, Rancher, Greenqloud Qstack, CoreOS, KVM, VMware, fuel, pcs/crm, Midokura, MySQL, Sensu, Terraform, Jenkins, GoCD, Ansible, Vagrant, Redis, Bash, Python, sed, awk, HipChat API, Slack API

• February 2015 – August 2015: Linux Systems Administrator at Trusted Builders, Seattle, USA.

Migrated computing infrastructure to the Cloud.

Skills used: Linux, Ansible, Vagrant, Rackspace Cloud, Nginx, Python

• May 2013 – January 2015: Linux Administrator II at Rackspace, USA.

Provided Cloud Support (servers, storage, databases, load balancers, etc.), administered Linux servers, Xen, XenServer, KVM, OpenStack, RESTful API, networking, site reliability, maintenance, LAMP-stacks, etc. Also helped develop tools and internal websites to help automate tasks (tools written in PHP, Python, and Django).

Skills used: Linux, Apache, MySQL, PHP, Python, Rackspace Cloud, Xen/XenServer, KVM

• December 2012 – March 2013: Cloud and web developer at MadLab, Seattle, USA.

Built a RESTful web framework and API using Amazon Web Services' NoSQL DynamoDB and a custom-built/in-house MVC in PHP.

• August 2012 – November 2012: Research Assistant / Scientific Programmer at the Dr. Elhanan Borenstein Laboratory — Department of Genome Sciences, University of Washington, Seattle, USA.

Conducted scientific research on the collection and organization of metagenomic datasets and the assembly of an analysis pipeline for metagenomic data; and

Analysis of the gut microbiome of children with cystic fibrosis (CF) and on methods to identify enriched functions.

Note: Everything was done in Linux and most of the programming was done in Python (+Pandas).

• October 2010 – June 2012: Consultant (Cloud and web developer / programmer) — Greater Seattle Area, USA.

Built a customer relationship management (CRM) website using Django (+Python, MySQL) with extended web services, command line interface, mobile apps, etc.

Note: Everything was done in Linux and/or Amazon Web Services (AWS), and most of the programming was done in Python.

• October 2006 – October 2010: Linux Administrator, Research Assistant, and software developer/maintainer at the Dr. Ethan A. Merritt Laboratory — Medical Structural Genomics of Pathogenic Protozoa Consortium, University of Washington, Seattle, USA.

Developed and maintained the Python Macromolecular Library (pymmlib) package and developed and maintained the TLS Motion Determination (TLSMD) webserver/webservices. Contributed code to the CCP4 suite. Performed detailed analysis of thousands of crystallographic structures (both in-house and from the PDB). Programmed in C, Fortran, Python, Perl, Javascript, Bash, etc., maintained multiple MySQL databases, and worked in a LAMP environment for web services. Research produced a paper published in a peer-reviewed journal (see below). Also was the Linux System Administrator for all computers in our lab, performed backups (tape, DVD, xHDDs, etc.), hardware and software support for all personnel, etc.

Note: Everything was done in Linux (and some Mac OS X) and most of the programming was done in Python.

• March 2006 – February 2007: Linux Administrator and Research Assistant at the Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA; (in absentia).

Developed an algorithm with a web services front-end to provide a quick estimate for protein-protein interactions and associated energies. Programmed in C, Fortran77, PHP and done in a LAMP environment. Research produced a paper published in a peer-reviewed journal (see below).

Note: Everything was done in Linux.

• August 2005 – November 2005: Research Assistant, Teaching Assistant, and programmer at the Dr. David W. Ussery Laboratory — Center for Biological Sequence Analysis, Danmarks Tekniske Universitet, Denmark.

Helped develop and maintain algorithms and web services for a Comparative Genomics department. Programmed in C, Perl, Python, Java, Bash, etc., maintained multiple MySQL databases, and worked in a LAMP environment. Also was a Teaching Assistant for a Comparative Genomics class. Research produced a paper publisher in a peer-reviewed journal (see below).

Note: Everything was done in Linux.

• October 2004 – July 2005: Research Assistant and System Administrator at the Dr. Carlos J. Camacho Laboratory — Center for Computational Biology and Bioinformatics, University of Pittsburgh, USA.

Modelled protein-protein and protein-DNA interactions from crystallographic data obtained via the Protein Data Bank. Developed and maintained 4 websites to provide access to the algorithms we developed as web services (all done in a LAMP environment). Programmed in C, Fortran77, Perl, PHP, and maintained multiple MySQL databases. Research produced 2 papers published in peer-reviewed journals (see below).

Note: Everything was done in Linux.

• Summer 2002 / December 2002: Research Assistant at the Dr. Alex Rich Laboratory — Department of Biology, Massachusetts Institute of Technology, USA.

Did research on the function of Z-DNA in various genomes and developed algorithms in C to search through genomes and compare the results against DNA microarray data. Also wrote Perl scripts and maintained a MySQL database.

Note: Everything was done in Linux.

• May 2000 – September 2004: Research Assistant and software developer at the Dr. P. Shing Ho Laboratory — Department of Biochemistry & Biophysics, Oregon State University, USA.

Did research on the function of Z-DNA in various genomes (resulted in a paper published in a peer-reviewed journal; see CV). Other duties consisted of being an assistant scientific programmer in C and Perl, as well as maintaining a MySQL database.

Note: Everything was done in Linux.

• September 1998 – April 2000: Lab Assistant for Kevin Krefft microbiology laboratory, Albany, OR, USA

Prepared all kinds of media (e.g., agar solutions and agar plates) to feed our stock of microbes, as well as rotating the colonies.

• December 1996 – December 1997: English Language Instructor at Berlitz, Ljubljana, Slovenia.

I taught at all levels (beginner, mid-level, and advanced). Most of my students were government officials, businesspersons, and other professionals.

• July 1996 – November 1996: Volunteer Humanitarian Aid Worker, Croatia.

I drove a van full of food and medical supplies to refugee camps on a nearly daily basis.

• September 1995 – June 1996: Audio Technician at Audio & Visual Production Centre, Tateyama, Japan.

My main role was to oversee a group of audio technicians, as well as performing automated dialogue replacement (ADR; aka "dubbing") for music videos, documentaries, etc.

• September 1994 – August 1995: Deputy Manager at a Pan-European Translation and Publishing House in both Vienna, Austria and Budapest, Hungary.

My main role there was as deputy manager of the audio and visual department. We would receive recordings of an original English audio or visual media translated into just about every language in Europe and then make thousands of copies of them (cassette tapes, CDs, DAT, VHS-PAL, VHS-NTSC, etc.) and then ship them all over Europe.