GARRET COX
(256) 415-ROOT(7668)
115 Luanne Ln
Muscle Shoals, AL 35661
garretwcox@gmail.com
www.garretwcox.com
· I am a Computer Science Ph.D. Candidate with a research focus on the application of High
Performance Computing to Bioinformatics. Research has involved multi-threaded, clustered, and GPGPU
approaches to Sequence Alignment.
· I have 6 years experience designing and implementing dynamic websites utilizing AJAX, clean and
efficient HTML with CSS, PHP with FastCGI, RoR with Mongrel, MS SQL Server and mySQL via IIS,
Apache, and nginx on Windows, Solaris, and Linux platforms.
· I have 2 years experience as an Administrator for a large, multi-platform, developer oriented
organization and 5 more years experience performing administrative duties for smaller organizations on a
contractual basis.
· I have nearly a decade of experience as an independent contractor, involved in every phase of software
development, including: establishment of user requirements, programming, testing, and debugging.
· I have certifications, and (more importantly) experience in network security auditing and digital
forensics.
· I have 15 years experience building, installing, and troubleshooting computers.
EXPERIENCE
Innuendosoft Corp (www.innuendosoft.com)
Muscle Shoals, AL
Vice President
Jan 2007-March 2010
· Deployed and administered a cluster of Ubuntu Xen guests via Slicehost and Amazon EC2 running
nginx, RoR with Passenger/Mongrel Cluster, PHP with FastCGI, Memcache, and Postgresql/MySQL. This
stack provides a secure, fast, and fault tolerant platform for both the corporate website and it's primary
project, VGRage (www.vgrage.com).
· Developed several RoR webapps making extensive use of AJAX (to enhance the user experience) and
Memcache (enabling the apps to withstand Digging or Slashdotting). Examples include:
· blogs with comment functionality
· photo albums which uploaded user's photos to Amazon S3 for fast, redundant content delivery
· a javascript focused character builder for the Star Trek Online videogame (stocb.vgrage.com)
· a ruby library which automatically remaps calls from Rails ActiveRecord to Amazon SimpleDB (which
I have open-sourced and made available at http://rubyforge.org/projects/activrecord2sdb/).
· Setup and administered 5 development machines featuring multiple bootable operating systems,
Windows and Linux based development environments and libraries, Virtualbox VM guests for testing, and
a file, print, and deployment server.
· Setup, administered, and used a Subversion/Git repository and Trac project management system in a
team environment.
Coldwell Banker Tennessee Valley Realty (www.cbtvr.com/)
Muscle Shoals, AL
Contractor
May 2004-March 2010
· Developed an application for Android based mobile phones for accessing their local idx.
· Installed and provided on-site tech support for Windows+Ubuntu client machines, Samba
login/fileserver, and wired/wireless network.
· Installed and provided on-site tech support for VOIP phones driven by an off-site FreeSwitch PBX I
deployed onto a Ubuntu Xen guest on Slicehost.
· Utilized Coldwell Banker infrastructure to set up the company's website.
Avalon Investment and Securities Group (www.avalonsecurities.com/)
Muscle Shoals, AL
Contractor
Sep 2007-March 2010
· Developed, deployed (via a Ubuntu/MySQL/Mongrel/nginx stack), and maintain a RoR web application
used internally by Avalon in the securities industry.
· Deployed and administered the Apache/PHP/MySQL server running the company's public facing site.
Provided technical support for the developer of the site.
· Provided on-site tech support for Windows client machines and wireless network.
Shane Vess Pest Control
Muscle Shoals, AL
Contractor
Feb 2010
· Developed an inventory system for internal use. You can browse an early demo of the system at
inventory.innuendosoft.com. Log in with the username/password demo/demo.
Dr. Larry Cox DMD (www.larrywcoxdmd.com/)
Muscle Shoals, AL
Contractor
Jan 2008-Nov 2008
· Provided on-site tech support for Windows Dentrix client machines, Windows Server, Microsoft SQL
Server, and wired network.
· Repaired a faulty Dentrix installation via recovering the old database from the SQL Server and
reinstalling the Dentrix server.
Xbox 360 Undelete Software
Muscle Shoals, AL
Personal Use
March 2009
· Created a C# application to undelete deleted files (game saves mostly) on an Xbox 360 harddrive and
memory card. I first had to determine the structure of the XTAF filesystem using a hex editor, as the
details of it's implementation are not publicly available.
Danielle McCann Photography(dmccannphotography.blogspot.com/)
Muscle Shoals, AL
Contractor
Feb 2009
· Recovered client photos lost due to filesystem corruption using the digital forensics tools Autopsy,
Sleuthkit, and foremost.
UAB CIS Department (www.cis.uab.edu)
Birmingham, AL
Ph.D. Research
2003-2007
· Developing Parallel/Vectorized implementations of the Smith-Waterman sequence alignment algorithm
via MPI clusters, Unix pthreads, Brook, MMX/SSE, NVIDIA CUDA, ATI CTM, IBM Cell, and SGI
Mitrionics, all in C/C++
National Scouting Reports (nsr-inc.com)
Birmingham, AL
Contractor
Nov 2007
· Setup and configured an IIS, PHP with FastCGI, and MS SQL environment on a Windows Server
machine for security, speed, and stability. Coded an “athlete search” PHP webapp which queried the
database according to user defined criteria and returned the results via a well formatted JavaScript/CSS
based interface.
Brother Bryan Mission (brotherbryanmission.com)
Birmingham, AL
Contractor
May 2007
· Designed an AJAX (JavaScript with HTML and CSS via DOM) website
SoD Listing System Parser
Personal Use
Jan 2007
Birmingham, AL
· Developed a data mining application in C# which sorted through the “Shards of Dalaya” listing system
(similar to a virtual stock market) and recommend good investments. Returns were “profitable”.
My Website (www.garretwcox.com)
Muscle Shoals, AL
Personal Use
Nov 2006
· Designed an AJAX (JavaScript with HTML and CSS via DOM) website
Virdaq (http://www.virdaq.com)
Birmingham, AL
Contractor
2003-2007
· Developed a LUA application used to create HTML profiles of a WoW character’s stats and gear.
Mob Mentality (site no longer active)
Birmingham, AL
Guild Member
2003-2007
· Coded various PHP webapps, such as a raid signup form and an attendance/dkp tracker which
members used to input and query data, as well as an administration backend. All functionality integrated
well with the phpBB2 forum providing “single login” functionality.
Plagiarism Checking Software
Birmingham, AL
Personal Use
2004
· Created software to compare student submitted papers against a database of reference material to
check for plagiarism in Visual Basic. Used while teaching.
Southtrust Bank (http://www.southtrust.com)
Birmingham, AL
Contractor
2003
· Developed VBA macros in Word and Excel used for tracking and organizing clients.
UAB CIS Department (www.cis.uab.edu)
Birmingham, AL
Assistant Administrator
Jan 2002-Dec 2003
· Managed 180+ public and personal access Windows, Linux, and Solaris machines, including
installation, setup, and maintenance of complex software development focused client configurations
involving Visual Studio, Eclipse, IIS, Apache, and various other esoteric software packages.
· Was the sole operator of the department’s Windows Server, managing Windows logins and network
storage; leveraged Active Directory, Group Security Policy, and VBScript to efficiently do my job.
· Also managed Linux logins, configuration, and storage via NIS and NFS, and utilized extensive BASH
and PERL scripting
· Led the creation of a new LDAP and Samba based server configuration allowing for unified logins and
storage across all 3 client OSes.
· Managed general networking tasks, such as Cisco router configuration, setting up DNS and DHCP
servers, implementing a VPN tunnel between the department and a remote location, configuring remote
user logins via SSH, and deploying the department’s first wireless network.
· Managed the department’s MS SQL and Oracle Database Servers.
· Provided Tech Support to Professors and Faculty.
UAB CIS Department (www.cis.uab.edu)
Birmingham, AL
M.S. Research
2001-2003
· Developed a biologic sequence recognition Support Vector Machine application in C/C++
· Coded an application in OpenGL to render biologic sequences in 3d.
· Created a Java GUI to feed data from an SQL database to the SVM mentioned above and display the
output via the OpenGL app.
· Developed various other bioinformatics applications in C, Perl, and Octave, including a Microarray data
parser and a heuristic multiple sequence alignment algorithm similar to CLUSTALW
· Coded various other applications using pthreads, MPI, and the standard Linux networking library for
various tasks such as a calculating prime numbers.
· Improved a chess playing AI
UAB CIS Department (www.cis.uab.edu)
Birmingham, AL
Instructor for Graduate Aid
2001-2002, 2004
· Taught C++ Programming and Discrete Mathematics as part of my graduate assistanceship.
Vicious Circle (site no longer active)
Birmingham, AL
Contractor
2000
· Designed a highly animated site using JavaScript and Dreamweaver
Samford University (www.samford.edu)
Birmingham, AL
Undergraduate Research
1998-2000
· Developed a Neural Network via Mathematica capable of pattern recognition.
· Created a LabVIEW frontend to send pictures from a CCD camera to the Mathematica backend. This
system was capable of surprisingly accurate facial recognition.
Silverfish Studios (www.3romans.com)
Birmingham, AL
Contractor
1998
· Created a physics model and error handling code for an online 3d racing game in Java
Law Firm (anonymous by request)
Birmingham, AL
Contractor
1998
· Designed an online database search tool using LabVIEW
EDUCATION
University of Alabama at Birmingham
Birmingham, AL
Ph.D. Candidate in Computer Science with an emphasis on Bioinformatics and HPC
· Level I exam completed.
· Research towards Level II exam still underway
University of Alabama at Birmingham
Birmingham, AL
M.S. in Computer Science with an emphasis on Bioinformatics and HPC, May 2003
Samford University
Birmingham, AL
B.S. in Mathematics, May 2000
· Minors in Computer Science and Chemistry
· Completion of Pre-Medical Curriculum
· Awards: Highest Sophomore GPA, Highest Mathematics GPA (All 4 years), Highest score on the
Putnam Mathematics Exam
· Member of the Mathematics and Pre-Med honorary fraternities
CERTIFICATIONS
· Certified GIAC Systems and Network Auditor
· SANS certified professional in Auditing Networks, Perimeters, and Systems
· SANS certified professional in System Forensics, Investigation, & Response
PUBLICATIONS
“Parallel Sequence Alignment Algorithms (Abstract)”, 2006 Graduate Student Research Days, March 2-3,
2006, University of Alabama at Birmingham, Birmingham, Alabama
“Sequence Alignment Algorithm: Multi-Dimension, Multi-Process (Abstract)”, 2005 Graduate Student
Research Days, March 3-4, 2005, University of Alabama at Birmingham, Birmingham, Alabama
Cox, Garret, “A Multi-Dimension Multi-Process Dynamic Sequence Alignment Algorithm (Abstract),”
Proceedings of the 81st Annual Meeting of the Alabama Academy of Science, March 17-20, 2004,
University of Montevallo, Montevallo, Alabama
Cox, Garret, ”IPCop Audit: A Home User’s Perspective,” GIAC Certified Professionals,
http://www.giac.org/certified_professionals/practicals/gsna/146.php, June 30, 2004
Cox, Garret, "Pattern Recognition with an Artificial Neural Network and a CCD Camera," Proceedings of
the National Conference on Undergraduate Research (NCUR) XIV, April 27-28, 2000, University of
Montana, Missoula, Montana
Cox, Garret, ”Pattern Recognition with Neural Networks,” Proceedings of the National Conference on
Undergraduate Research (NCUR) XIII, April 8-10, 1999, University of Rochester, Rochester, New York
PRESENTATIONS
“Parallel Sequence Alignment Algorithms”, 2006 Graduate Student Research Days, March 2-3, 2006,
University of Alabama at Birmingham, Birmingham, Alabama
“Sequence Alignment Algorithm: Multi-Dimension, Multi-Process”, 2005 Graduate Student Research
Days, March 3-4, 2005, University of Alabama at Birmingham, Birmingham, Alabama
“A Multi-Dimension Multi-Process Dynamic Sequence Alignment Algorithm,” 81st Annual Meeting of the
Alabama Academy of Science, March 18, 2004, University of Montevallo, Montevallo, Alabama
"Pattern Recognition with an Artificial Neural Network and a CCD Camera," National Conference on
Undergraduate Research (NCUR) XIV, April 27-28, 2000, University of Montana, Missoula, Montana
”Pattern Recognition with Neural Networks,” 79th Annual Meeting of the Mathematical Association of
America (MAA) Southeastern Section, March 10-11, 2000, UNC Charlotte, Charlotte, North Carolina
”Pattern Recognition with Neural Networks,” National Conference on Undergraduate Research (NCUR)
XIII, April 8-10, 1999, University of Rochester, Rochester, New York
”Pattern Recognition with Neural Networks,” 78th Annual Meeting of the Mathematical Association of
America (MAA) Southeastern Section, March 12-13, 1999, Rhodes College, Memphis, Tennessee
SKILLS SUMMARY
· Deployment of IIS/Apache/nginx, PHP with FastCGI, RoR with Mongrel Cluster, and
mySQL/Postgresql/MS SQL Server on Linux/Windows.
· Optimizing the site configuration for speed and stability via load balancing, Memcached, and writing
code that only uses PHP/RoR to render a small portion of the page which is served via SSI/AJAX
· Securing the site via proper firewalling, using limited web access accounts at every step, and sanitizing
form/database inputs in the code.
· Coded with PHP, RoR, BASH, Perl, VBScript, JavaScript, and LUA
· AJAX (Javascript with HTML,CSS, and XML via DOM) development in both Aptana and Dreamweaver
· Clean, well documented code that is easily portable due to the use of standardized interface libraries
such as ADODB.
· Adherence to the MVC programming model, using the Smarty template engine in PHP, and separating
design from structure via correct usage of CSS.
· Developing for mobile devices, most notably the android
· Extensive experience coding various Bioinformatics algorithms on a variety of platforms
· Developed high performance applications via MPI clusters, Unix pthreads, Brook, MMX/SSE, NVIDIA
CUDA, ATI CTM, IBM Cell, and SGI Mitrionics, all in C/C++
· Optimized applications in x86 assembly, as well as written simple applications from scratch
· Used Visual Studio to write Visual Basic (6.0 and .NET), C/C++ (MFC and .NET), and C# applications
for Windows
· Used Eclipse to write Java and C/C++ applications for Windows, Linux, and Solaris
· Comfortable with GNU command line tools for administration (ex. chmod) and development (ex. make)
· 3d graphics via OpenGL and DirectX
· High end mathematics and basic physics programming in C/C++, Mathematica, Maple, and Octave
· Experience using LabVIEW to interface with laboratory equipment and robotics. Experience coding
large, complex programs in LabVIEW, as well as interfacing with dlls allowing for interoperation with other
programs and platforms.
· Developed pattern recognition algorithms and AI
· Experience with low level networking programming. I know what a buffer overflow is and how to prevent
it in my code.
· Set up advanced MS Office configurations using VBA
· Subversion use and administration
· Linux and Solaris administration utilizing NIS and NFS
· Windows administration utilizing Active Directory and Group Security Policy
· Cross Platform integration experience utilizing LDAP and Samba
· Networking experience including DNS, DHCP, and SSH servers, as well as setting up VPNs and
wireless access points and repeaters with encryption
· Automating deployment of a large number of machines
· Network Security Auditing, including building and deploying “hardened” versions of various linux
distributions, applying “gold standard” security policies to windows, and securely structuring networks by
deploying appropriate firewalls, monitors, dmzs, and honeypots.
· Digital Forensics, including file recovery, partition and filesystem rebuilding, intrustion detection.
· Image creation and optimization with Adobe Creative Suite and GIMP
· Sound editing with Cakewalk Sonar
· Video encoding with RealMedia, Quicktime, Windows Media, and ffmpeg
· Experience as an independent contractor and working in a team environment
· Tech Support
· Teaching