Algorithmen der Bioinformatik

BIOINF4998 Research Project Bioinformatics

This page describes the research projects available in the Algorithms in Bioinformatics group.

For other research projects, please visit: Applied Bioinformatics and Integrative Transcriptomics.

Course BIOINF4998 Research Project Bioinformatics, SoSe 2018
Supervisor Prof. Daniel Huson  and all members of the lab
Dates ~25 days, April - Sept 2018
Applications Please apply by April 15th
You will be notified by April 20th

Email to: Prof. Daniel Huson, see below for details
Language English
Links Campus

The course "BIOINF4998 Research Project Bioinformatics" provides the student with the opportunity of doing research work in our group for the duration of six months, working on average one day a week.  You will work closely with members of the lab, participate in weekly lab meetings and a desk in C207 will be provided. It is a good opportunity for those considering a PhD or scientific career.

Participation is by application only. If you are interested in participating in this course, then please send an email to Prof. Daniel Huson stating 

- which of the three topics below you are interested in,

- briefly explain why you are interested in the topic,

- which of the prerequisite courses you have taken (with grades), and

- the desired "format" of your participation, that is, the start and end date, and days per week

The number of participants is limited to three and there are three topics on offer in this semester:

Support in SplitsTree5 development

We are currently writing a new implementation of our widely used SplitsTree4 program. The new program, SplitsTree5, is based on  JavaFX. This is a program for phylogenetic analysis, You’d be asked to program in Java, research phylogenetic algorithms and UI design. A concrete contribution would be to implement a powerful interactive alignment editor that is integrated into SplitsTree5.  

Prerequisite courses: 

- BIOINF4399 Advanced Java for Bioinformatics and 

- either BIOINF4110 Sequence Bioinformatics or BIOINF2110 - Grundlagen der Bioinformatik

Python package for metagenomic analysis tools

In the context of microbiome analysis, our lab has established a pipeline that consists of running the alignment tool DIAMOND to compare metagenomic sequencing reads against the NCBI-nr protein reference database and then running the Meganizer tool to add taxonomic and functional classifications to the resulting DIAMOND DAA file. A meganized DAA file can then be opened in the interactive microbiome analysis tool MEGAN or queried using the MEGAN command line tool DAA2INFO. The project goal is to write a python package that provides access to the content of a meganized DAA file, and then to demonstrate how to use the package so as to allow python-based analysis of the data.

Prerequisite courses: 

- BIOINF4322 Seminar Microbiome Analysis or BIO4399 - Computational microbiome analysis 

- BIOINF4110 Sequence Bioinformatics or BIOINF2110 - Grundlagen der Bioinformatik

Tutorials development

Our lab has produced a number of software tools that are routinely used by life scientists. Two of these tools, MEGAN and SplitsTree, in particular, provide a large number of options and can be applied to numerous different use cases. The project goal is to develop a suite of tutorials that address the most common use cases of the two tools. This work will involve performing a survey of papers that use the tools so as to establish the most common use cases and also to produce example data from such publications. These tutorials will be integrated into our two community pages and

Prerequisite courses: 

- BIOINF4110 Sequence Bioinformatics or BIOINF2110 - Grundlagen der Bioinformatik

- Helpful: a course on microbiome analysis and/or phylogenetic analysis

LPs and grading

You will receive 9 LP for completing this course. Your grade will be based on the quality of the research work that you performed and on general aspects of your performance as a lab member (motivation,  communication skills and reliability).