Başak Abak

Software Engineer
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About me

In my position as a Bioinformatician and Software Enginner for Istanbul Medipol University, I played a role in building an automated pipeline for variant analysis on WES data. We used bioinformatics tools and databases for this project. I also developed a desktop application for variant analysis and reporting which is currently used in Medipol MEDIGEN Lab. Also I’m developing it’s equivalent web interface. Lastly, I’m working on the database management of Medipol patients variations.

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Education


Sep. 2019 – Present
now

Masters of Science

Department of Bioinformatics, 100% English, Muğla Sıtkı Koçman University, Muğla, Turkey

GPA: 4.0/4.0

Supervisor: Tuğba Önal Süzek, Assistant Professor, Ph.D

Master Thesis: TCGAnalyzer: Developing of a web portal for visualization of pan-cancer molecular patient data TCGAnalyzer

Sep 2015 – Jun 2019

Bachelor of Science

Department of Computer Engineering, 100% English, Muğla Sıtkı Koçman University, Muğla, Turkey

GPA: 3.65/4.0

Supervisor: Tuğba Önal Süzek, Assistant Professor, Ph.D

Bsc Thesis: A Tactile mobile game that recognizes Turkish alphabet letters for teaching reading to children , implemented using OpenCV Github

Sep 2016 – Jun 2017

Erasmus Program(1 year)

Department of Computer Science, Vsb-Technical University of Ostrava,Ostrava, Czech Republic

Sep 2014 – Jun 2015

Certificate of English Proficiency

School of Foreign Languages, Muğla Sıtkı Koçman University, Muğla, Turkey

Work Experience


2 Sep. 2019 – Present
now

Researcher - Software Engineer - Bioinformatician

Regenerative and Restorative Medicine Research Center, Istanbul Medipol University, Istanbul, Turkey

Director: Gürkan Öztürk, Professor, MD

Supervisor: Barış E Süzek, Assistant Professor, Ph.D

  • Building an automated pipeline for variant analysis on WES data, which is being used on IBM high performance computing cluster
  • Developed a desktop application for variant analysis and reporting which is currently used in Medipol MEDIGEN Lab (Javascript, NodeJS, HTML, CSS, Electron, SqLite)
  • Developing a web interface for variant analysis and reporting for Medipol MEDIGEN Lab stuffs to use (React, NodeJS, MySQL, HTML, CSS)
3 July 2018 - 3 Sep 2018

Summer Intern

Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey

Advisor: Tuğba Önal Süzek, Assistant Professor, Ph.D

  • Developed an R-Shiny based desktop application for aid in loading and filtering of large human variation summary data(Annovar output)
  • Developed and R-Shiny based application that executes a TCGA differential gene expression analysis pipeline.
3 June 2018 - 3 July 2018

Summer Intern

Türk Telekom,Ümraniye,İstanbul

Advisor: Muhittin Altınel

  • Developed a demo android application for Türk Telekom’s staff to use.

Articles

Projects

Bioinformatics

TCGA Drug Finder

R Javascript CSS

Gamification

Virtual Hospital Game

C# Unity

GUI

Library App

Java SQLite

Database Management

Nutrition Facts for McDonald’s Menu Database

MySQL MySQL WorkBench

Design of Applications for Mobile Devices I

A game like mario

Javascript HTML CSS

Web Development

Houston Rockets basketball team page

Django Python Javascript HTML CSS

Web Mining

A web server to show top ten music of specific country

R Shiny

Dynamic Web Development

E-commerce web site

Php Javascript HTML CSS

Bash & R Scripting, Data Mining

Building an automated pipeline for variant analysis on WES data, which is being used on IBM high performance computing cluster

R Bash Scripting HPC

Desktop Application

Developed a desktop application for variant analysis and reporting which is currently used in Medipol MEDIGEN Lab

NodeJS Javascript HTML CSS SQLite Electron

Web Interface Development

Developing a web interface for variant analysis and reporting for Medipol MEDIGEN Lab stuffs to use

ReactJS NodeJS Javascript HTML CSS SQLite MySQL

Honors and Awards
Health Institutes of Turkey (TUSEB) Scholar (2 years)(2019- continue): Development of a Web Platform for Drug Repositioning Analysis Specific to Cancer Cohorts Using Genetic, Transcriptomic and Survival Data.

Achieventment
2018-2019 top scoring student in the department and 3rd placed in engineering faculty.

Poster Presentations
Abak Başak, Süzek Tuğba, 2019. TCGA Drug Summary Interface. Poster presentation, Big Data Training School for Life Sciences Second edition - EU COST CHARME, Mar 4-8, 2019, Athens, Greece
Abak Başak, Süzek Tuğba, 2019. TCGA Drug Summary Interface. Poster presentation, HIBIT2019, Oct. 2019, İzmir, Turkey

References
Dr. Tuğba Önal-Süzek
Prof. Dr. Gürkan Öztürk
Dr. Barış Ethem Suzek
Dr. Akif Ayaz