Senior Bioinformatics Analyst · PolyGenyx, Inc.
Analizing of chromatograms produced from DOP-PCR and PCR to detect SNPs using Sequencher, Phred, Phrap, Consed and self-coded software.
Wrote a program (Windows) to rename and sort received chromatogram files into a standard format for further processing.
A similar script was coded for sorting chromatograms analyzed under Linux.
Installed one ADR-30 (IDE) and two ADR-50 (SCSI) tape backup drives. The ADR-30 was put to use on the primary BioInformatics workstation and performed in Linux (backing up the Windows partitions also). One ADR-50 was configured as an external SCSI device and setup on an SGI O2 machine used for scanning MicroArrays. The second ADR-50 was configured as an internal SCSI device on the Windows NT 4.0 Server.
Evaluated many backup software solutions for the above drives. Eventually choosing, installing, and configuring Windows NT 4.0 Server (Veritas Backup Exec), SGI Irix 6.5.x (BRU/xBRU), and Red Hat Linux 6.x & 7.x (BRU/xBRU). Installed TCL/TK on the Irix box for xBRU to function.
Evaluating and recommending MicroArray analysis software to determine which would best suit the needs of the company (accuracy, speed, statistical output available, etc.). Among those configured and tested: Imagene, Autogene, ScanAlyze, and others.
Performming analysis of MicroArray scans using primarily, ImaGene from BioDiscovery.
Evaluation and statistical analysis of MicroArray scans performed with a laser scanner vs. the same slides scanned by the ArrayWorx scanner.
Attended a 3 day training seminar by BioDiscovery on MicroArray analysis.
Attended a 4 hour BioTech seminar in Boston relating to hardware & software needs and solutions.
PolyGenyx needed a printer for the SGI O2 machines. Typical cost of a color printer certified for these machines was about $5,000. I researched and implemented a $500 network color printer solution (using Ghostscript under Irix). Beyond the immediate cost savings, an added bonus was the ability to print to it from any machine on our LAN.
Configuring every computer on the LAN as a VNC server (running in the backround). This allowed remote access to each machine from any authorized desktop/user regardless of Operating System. The Chief Scientific Officer could, while booted into Windows, access a Linux machine and use its software as if he were sitting right at the Linux machine. I could access the Windows NT 4.0 Server (or any other machine) to (for example) restart the printer spooler without having to leave my office. Also, since the entire LAN was behind a firewall, I configured the firewall to give me secure access via VNC to my workstation from the Internet (think: work-from-home). Having access this way to a single machine gave me access to them all.
Configuring and mantaining the WebRamp 700s firewall.
Attended weekly scientific meetings to report progress on current projects, thoughts on future projects and or new directions for current projects, and receive further project direction as determined by management
Maintained a close and continuing communication link with the Chief Scientific Officer to reach company goals. My ability to multi-task many on-going projects was a necessity in an environment where priorities might change quickly, and maintaining open communication with the CSO helped adjust project priority in a very timely manner.
Configured clock adjusting software on all of our LAN machines. For example, Atomic Time was used on the Windows machine to correct the clocks from going ascew, as they were wont to do.
AntiVirus software was configured and updated on a monthly basis for all of the Linux and Windows machines. Norton Antivirus for Windows; FileScan for Linux.
Maintainning communication with our ISP for correcting any Internet connection problems.
I maintained and updated our company web site. Posting updates to it as provided by the Senior Scientist (the company's lead scientific writer). Also, contacted Network Solutions, ISPs, etc. to correct a DNS issue that temporarily directed people from www.polygenyx.com to an incorrect IP address.
Researched, download, compiled, installed, and configured cdrecord and Xduplicator on an SGI O2 machine for moving large image files to CD-ROM storage.
Updating of Operating Systems (Irix, Windows98SE, Linux, WindowsNT4 W/S) with security patches and bug fixes on a monthly basis (more often if necessary).
Upon downsizing of the company, I configured a multi-drive, multi-partition, multi-boot computer to essentially perform the same duties as the most important workstations on the LAN.
Providing detailed write-ups of some of my work on electronic DOP-PCR to Senior Scientist for use in a grant application and to the Chief Scientific Officer for inclusion in "Genome Complexity Reduction for SNP Genotyping Analysis" (see Publications, below)
Submitted daily activity/progress reports to the Chief Scientific Officer and to the Senior Scientist.
Configured all of the company's e-mail clients. And, through communication with our ISP, maintained the employees' POP3 e-mail boxes.
Performed data recovery (once following an e-mail virus infection and once after files that had failed to copy to a Zip disk were deleted) for the company President & Chief Executive Officer.
Maintaining LAN workstations and servers by running Scandisk, Defrag, Diskeeper, and other utilities during times when those machines were otherwise not being used.
Configured a second Windows NT 4.0 Server for temporary use in our LAN.
Provided supervision and assistance to a student of BioInformatics who interned with us.
Co-designed, with the Chief Scientific Officer, for professional printing, using Photoshop 5.0, a poster used for presentation of our techniques.
Performing web based BLAST searches
Reviewed and analyzed the database work done by an outsourced company. Their work was found to be substandard (or completely non-standard, these database "professionals" didn't even know what the term "Third Normal Form" meant). This lead to their entire (never functional) system being scrapped.
Designing, implementing, and updating of a PostgreSQL database to track our experimental SNP findings. The database contained a copy of the Human Genome from the NCBI, the capability to store other genomes as well, and much of the data relating to the experiments. I designed all of the client interfaces to make the database useful. And, coded a combination of shell scripts, Perl, and C to input vast amounts of data output from a variety of programs into the database.
Coding programs to simulate laboratory experiments; predict experimental results; and developed an electronic DOP-PCR simulator – results from which would pipe directly into the aforementioned database.
Writing and reviewing scripts to control some of our robots. The robots I worked with include a Biomek 1000, a Biomek 2000 (both from Beckman Coulter), a ProSys 5510 Microarray Analyzer and PegaSys 150 Stacker (from Cartesian Technologies), and an ArrayWorX Fluorescence Slide Scanner from Applied Precision Instruments. And, the setup of Bar Code scanners for (planned) tracking and database interfacing.
Working with other software (some not mentioned above), including: BLAST cl3, Primer3, RepeatMasker, Dapple, Lview, ACDC, Netscape Messenger, Microsoft Office 2000, StarOffice 5.1 & 5.2 (Linux and Windows), Opera 5.x (Linux and Windows), Photoshop, and more...
