Mehmet Tekman

Contact
CV + Academia

Hey. This is a little static profile. It’s by far not everything, but I’ve included repos of mine that I either dedicated a lot of time to, or am proud in some teeny tiny way. Click the badges above for links to my public profiles.

[In Brief]

[In Essence]

Languages + Frameworks	Daily Drivers
Languages Frameworks	Android Desktop

[In Detail]

Work

Enterprise Software

Galaxy

• tools-iuc - The tool recipe repository: 58 closed and 6 open pull-requests
• galaxy - The core dev repository: 5 closed and 1 open pull-request
• training-material - The teaching materials repository: 37 closed pull-requests

Analysis

Linkage and Haplotype Analysis

• HaploForge - A Comprehensive Pedigree Drawing and Haplotype Visualisation Web Application.
• Linkage Pipeline - Linkage Analysis pipeline for both Autosomal and X-linked penetrances.
• poster-haploforge - Latex poster for Haploforge
• phd-thesis - Latex of PhD Thesis

Variant or Sequence Analysis

• OVAS and OVAS-maker - Open-source Variant Analysis Suite, and ISO maker.
• ngs-pipeline.sh - Skeleton for NGS pipeline, now backbone of OVAS project.
• bedtarget - Grabs regions of genetic context from UCSC databases and reformats them as BED files.
• genepender - Annotates (often overlapping) BED-defined regions to variants in a VCF file. Used for providing a gene/exon context to variants.
• funcannot - Annotates cDNA, protein, mutation type, and other funcational changes to variants in a genepender’d VCF file

Genome-wide Association Studies

• MembranousScripts - Set of utilities used to perform basic allele testing and parallel processing of LocusZoom plots

Other

C++ based

• motiondetect - An FCam-based CImg motion-detector for Maemo devices. MSci Thesis.
• PreciseChisq - An example curses program tied in with PAM authentication that executes upon (maxtry) failure

Bioinformatic

• bamcover - Performs basic pileup statistics of BAM files, depth and coverage.
• RefGeneStats - Human Genome Exon/Intron statistics from refGene
• comparing-matrices-mine-grun - A comparison of the count matrices produced by Galaxy CelSeq2 workflow, and that by MPI perl scripts, particularly with attention paid to the number of repeating elements

Hobbies

Leisure

Cycling, Snowboarding, Wandering. Usually do all in an ill-equipped care-free fashion. I should probably add something useful here. Oh well.

Emacs

My pride and joy. Small and friendly community I love to contribute to.

General Packages

• emacs config - My Emacs config, constantly updated, broken, updated.
• elisp-depmap.el - Writes out a graphviz map based on project functions
• remind-bindings.el - Reminders for your init bindings
• terminal-toggle.el - Elisp package for toggling a terminal
• wiki-drill.el - Elisp library to convert wiki-summary texts into org-drill
• [WIP] planemo-mode.el - A mode to generate Galaxy XML tool files

Org-Mode Packages

• org-mode-manager - A tree-like management tool for your org-mode files
• org-treeusage.el - Examine the density of org headings
• org-treescope.el - Provides a time and priority based sparse tree interaction mode
• org-tanglesync.el - Sync changes between internal org-mode source blocks and tangled files
• org-calories.el - A calorie tracking food and fitness package for logging your intake/outtake

Random

Productivity

• ZoteroGoogleDrive-PDFLinker (Local) and (Cloud) - Unites your GDrive storage with your Zotero database.
• ShellUtils - Shell functions and scripts for general work (and play) use.

Security

• PAM-curses-warning-formatter - An example curses program tied in with PAM authentication that executes upon (maxtry) failure
• iptables-autobanner - Checks journalctl logs for forced entry and adds malicious ip to the iptables ban list, run ideally with cron.

Games and Javascript Demos

• Slidey - HTML5 Slides Creator and Editor
• diaspora-installer - Installer for the BattleStart Galactica Diaspora mod of the FreeSpace2 game
• runescape-motiondetector - Looks for mineable items in Runescape using OpenCV Blob detection, and autoclicks them in X11
• P2 Raycast Demo - Raytracing test using Canvas and pixiJS
• TreeDemo - Messing around with generational trees. For a much more professional outlook, see the Benchmark test in HaploForge.

Other

• PyFlogger - CLI python food logger and calorific content displayer
• AlbumMaker - Automates anonymous album creation using a dragndrop interface with unix backend.
• maemo-alarm - Commandline tool to interface with alarmd library on maemo.

TODO:

• Add teaching contributions
• Add single cell projects