Alumni

Former employees and students of the workgroup

Research Assistants

Mahdi Sadeghi

MSc in Computer Science
Sand 14 ⋅ Office C107

72076 Tübingen
Germany

 +49-7071-29-70452
 +49-7071-29-5152
mahdi.sadeghispam prevention@uni-tuebingen.de

Participation

December 2019 to May 2020

Project

Development of essential software and resources for the scientific community for systems biology modelling via Java™

Further information

Thorsten Tiede

MSc in Bioinformatics
Sand 14 ⋅ Office C107

72076 Tübingen
Germany

 +49-7071-29-70452
 +49-7071-29-5152
tiedespam prevention@informatik.uni-tuebingen.de

Participation

December 2019 to April 2020

Project

Development of essential software and resources for the scientific community for systems biology modelling via Java™

Further information

GitHub profile

 

 

Thomas M. Hamm

Biologist (t.o.)

Participation

November 2016 to November 2019

Further information

Personal website
GitHub profile

Student assistants

David E. Vetter

BSc in Bioinformatics

Participation:
October 2019 to April 2020

Further information

GitHub profile

 

Antonia I. Schuster

MSc in Biology

Subject: Bioinformatics

Participation:
October 2019

Maria E. Heitmeier

Subject: Cognitive science

Participation:
April to August 2019

Further information

GitHub profile

Anton J. Rabe

Subject: Cognitive science

Participation:
November 2018 to April 2019

Further information

GitHub profile

Christoph Blessing

Bachelor in bioinformatics

Assistance:
November 2017 to
February 2018

Thesis

Development of an interactive graphical editor for systems biology models

Graduation: September 2017

Further information

GitHub profile
LinkedIn profile

Veronika Kohler

Bachelor in media informatics

Assistance:
May to August 2016

Further information

LinkedIn profile

Master students

Marietta Hamberger

BSc in Computational Linguistics

Research Project

Graphical editor for systems biology models

Expected completion
April 2020

Further information

LinkedIn profile

Lina Widerspick

Subject: Molecular Medicine

Research Project

Reconstruction of Dolosigranulum pigrum 

Defense:
March 16th 2020

 

Pia Rautenstrauch

Subject: Bioinformatics

Research Project

Reconstruction of Moraxella catarrhalis BBH18

Defense:
September 10th 2019 in C118a

Silvia Morini

Field of study: biology

Thesis

Genome-scale metabolic network reconstruction of the pathogen Treponema pallidum ssp. pallidum

Graduation: September 2018

Further information

LinkedIn profile

Marc Alexander Voigt

Field of study: bioinformatics

Thesis

Representation of ME-models in SBML

Graduation: June 2018

Further information

GitHub profile

Bachelor students

Manuel Dienert

Major: Bioinformatics

Thesis

Derivation of gene-protein reaction rules

Expected completion:
February 2020

Further information

GitHub profile

Manuel O. Harke

Subject: Bioinformatics

Thesis

Visual analytics of clinical multi-omics data in biological networks

Co-mentor:
Jun.-Prof. Dr. Michael Krone

Expected completion:
August 2019

Further information

GitHub profile

 

Niklas Henle

Subject: Computer Science

Thesis

Expanded genome-scale model of Haemophilus influenzae

Graduation: September 2019

Further information

GitHub profile

Robert Deibel

Subject: Bioinformatics

Thesis

Development of an editor for large-scale biochemical models

Graduation: March 2019

Further information

GitHub profile

Roman Schulte

Field of study: computer science

Thesis

InSilico - Concept of a Modular Research Environment
Graduation: August 2018

Project within the Google Summer of Code 2016

JSBML Validation System

Mentors:
Jun.-Prof. Dr. Andreas DrägerDr. Sarah M. KeatingDr. Michael Hucka, and Nicolas Rodriguez

Participation: May to August 2016

Further information

GitHub profile
Personal homepage

Lisa Falk

Field of study: bioinformatics

Thesis

Valiation and Simulation of Qualitative Models

Graduation: February 2018

Further information

GitHub profile

Lea F. Buchweitz

Field of study: cognitive science

Thesis

Dynamic visualization of metabolic networks

Graduation: September 2017

Further information

GitHub profile
LinkedIn profile
ResearchGate profile

External Students

Google Summer of Code and the NRNB Academy repeatedly fund several of the research group's software products. These programs allow international students to join the team and actively participate in the development of open source software.

Google Summer of Code 2019

Nikhil Ghodke

Subject: Computer Engineering (B.Sc.)
Affiliation: Vishwakarma Institute of Technology, Pune

Project

Erstellsystem für das Plugin-Framework “InSilico”
Quellcode auf GitHub

Participation: April to September 2019

Mentors

Roman Schulte and Jun.-Prof. Andreas Dräger

Further information

Project blog
PivotalTracker
GitHub profile
Twitter channel

Kaustubh Trivedi

Subject: Computer Science and Engineering (B. Tech.)
Affiliation: Indian Institute of Technology, Roorkee

Project

Extending ModelPolisher to a universal model annotation tool
Source code on GitHub

Participation: April to September 2019

Mentors

Jun.-Prof. Andreas Dräger,
Thomas J. Zajac, and Dr. Matthias König

Further information

Project blog
GitHub profile
Twitter channel

Bhavye Jain

Subject: Computer Science and Engineering (B. Tech.)
Affiliation: Indian Institute of Technology, Roorkee

Project

Validierung räumlicher Modelle der Systembiologie in Java™
Quellcode auf GitHub

Participation: April to September 2019

Mentors

Nicolas Rodriguez, Thomas M. Hamm, and Lucian P. Smith, Ph.D.

Further information

Project blog
GitHub profile
Twitter channel

Google Summer of Code 2018

Shalin Shah

Target degree: Ph.D.

Affiliation: Duke University, Department for Electrical and Computer Engineering, NC, USA

Project

Simulating systems biology models in Java™

Participation: April to August 2018

Mentors

Jun.-Prof. Dr. Andreas Dräger and Dr. Matthias König

Further information

Project blog
GitHub profile

Google Summer of Code 2017

Takhiro Yamada

Current position: Research associate

Affiliation: Keio University, Institute for Biosciences and Informatics

Project

Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models

Participation: April to August 2017

Mentors

Jun.-Prof. Dr. Andreas Dräger, Kaito Ii, and Dr. Matthias König

Further Information

Project blog
GitHub profile
ResearchGate
ORCID

Google Summer of Code 2016

Tramy Nguyen

Position: Ph.D. student

Affiliation: University of Utah at Salt Lake City, UT, USA

Project

Interconversion between the systems biology modeling formats SBML and BioPAX

Participation: May to August 2016

Mentors

Dr. Michael HuckaJun.-Prof. Dr. Andreas DrägerProf. Dr. Chris J. Myers, Prof. Dr. Akira Funahashi, and Nicolas Rodriguez

Further Information

Project blog
GitHub profile

Hovakim Grabski

Kaito Ii

Position: Ph.D. student

Affiliation: Keio University, Institute for Biosciences and Informatics, Japan

Project

Interconvertible Layout software for CellDesigner

Participation: May to August 2016

Mentors

Prof. Dr. Akira FunahashiJun.-Prof. Dr. Andreas DrägerNicolas Rodriguez, and Dr. Michael Hucka

Further Information

Project blog
GitHub profile
LinkedIn profile

Devesh Khandelwal

Subject: Information technology and mathematics

Affiliation: University of Delhi, Delhi, India

Project

Visual Biology with Escher

Participation: May to August 2016

Mentors

Zachary A. King and Jun.-Prof. Dr. Andreas Dräger

Further Information

Projekt blog
Projekt wiki
GitHub profile