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Application Workshop 2014
June 30 & July 1, Bielefeld University
Sunday, June 29 (Arrival)
You are welcome to join an informal dinner with some local students. We will meet from 7pm in the restaurant Mexim's, which is next to the back entrance of the main train station. It is no problem if you come later. (Unfortunately, we cannot invite you this time.)
Monday, June 30 (Presentations)
Room: G2-104 in the CeBiTec building
| Time | Speaker | Title | Project |
| 9.00 - 9.15 | - | Welcome coffee | - |
| 9.15 - 10.35 | N. A. | Deciphering Deep Biosphere - Computational Analysis of Metagenomics sequences | 1 |
| G. D. | A probabilistic method for constructing phylogenetic tree for a given collection of sequences | 1 | |
| V. Q. | Database Visualization | 5 (1) | |
| L. Z. | CellWhere: adding sub-cellular localization to functional association networks | 5 | |
| 10.35 - 11.00 | - | Break | - |
| 11.00 - 12.20 | S. K. | Clustering and Visualization of Polyomics data | 5 (8) |
| O. Y. | Hierarchical clustering of NGS data of immunoglobulins | 5 (7, 9) | |
| L. H. | Rep-Seq, approaching Ultimate Diagnoses | 8 (9) | |
| T. Z. | Adapting the jumping alignment for reconstructing the modular recombination history of phages | 9 | |
| 12.20 - 1.45 | - | Lunch | - |
| 1.45 - 3.20 | Roland | DiDy - An overview | - |
| S. F. | Development of Human Mitochondrial microRNA database | 2 | |
| J. Y. | Analyze large collections of NGS data based on the integration of Apache Hadoop, HBase and Hive | 2 | |
| K. K. | Spatio-Temporal Convolutions Kernels for Trajectory Clustering | 4 (3) | |
| M. L. | Machine Learning for Big Data in Biomedical Research | 4 | |
| 3.20 - 3.40 | - | Break | - |
| 3.40 - 5.00 | D. M. | Reconfigurable Discrete Controller Synthesis for Multi-agent Coordination based on Individual Specifications | 3 |
| E. B. | Automated analysis of mass spectra: application to the detection of traces of explosive molecules in fingermarks | 6 | |
| A. G. | Assembly and comparative analysis of the Genome of Acaryochloris marina HICR111A | 7 | |
| G. H. | Pattern recognition in a heat maze based spatial system adapted to Drosophila melanogaster | 7 | |
| 5.00 | - | End | - |
| 7.00 | - | Dinner | - |
Tuesday, July 1 (Interviews)
Rooms: U10-146 (interviews) and U10-155 (coffee, common room) in the University main building
| 8.30 - 8.45 | Welcome coffee | |
| 8.45 - 10.15 | G. H. | Project 7 |
| A. G. | Project 7 | |
| E. B. | Project 6 | |
| D. M. | Project 4 | |
| M. L. | Project 3 | |
| K. K. | Project 3, 4 | |
| 10.15 - 10.30 | Break | |
| 10.30 - 12.00 | J. Y. | Project 2 |
| S. F. | Project 2 | |
| T. Z. | Project 9 | |
| L. H. | Project 8, 9 | |
| O. Y. | Project 5, 7, 9 | |
| S. K. | Project 5, 8 | |
| 12.00 - 1.00 | Lunch | |
| 1.00 - 2.00 | L. Z. | Project 5 |
| V. Q. | Project 1, 5 | |
| G. D. | Project 1 | |
| N. A. | Project 1 | |
| 2.00 | End (for applicants) | |
| 4.00 | Faculty meeting |
Projects
- Ancestral lines under selection: Linking population genetics and phylogenetics (Baake)
- Bioinformatics platform for high-throughput pangenome data analysis (Goesmann, Sczyrba)
- Feature selection and relevance learning for high dimensional biomedical data sets (Hammer)
- Efficient grouping and cluster validity measures for NGS data (Hammer)
- Framework for the systematic development of biological networks (Hofestädt)
- Integrative analysis of mass spectrometry-based omics data (Nattkemper, Albaum)
- Interpretation and visualization of molecular dynamics in complex bioimage data (Nattkemper, Albaum)
- Cloud-based Bioinformatics Frameworks for NGS Data (Sczyrba, Goesmann)
- Computational methods for functional analysis of a pangenome (Stoye, Albaum)
Participants
For reasons of privacy, only the candidates' initials are listed here. (internal page)
Presentations
- Please contact the supervisor(s) for further reading and discussing the perspective project.
- 15 minutes presentation, 5 minutes questions/discussion. Since we have a tight schedule, stay in time!
- Shortly present your CV (one slide should be enough): Where/what did you study? Biology or computer science background? Research interest? …
- Main focus on your previous scientific work - usually your Master's project.
- A few minutes about the prospective PhD project.
- A laptop will be provided. Your slides should be in PDF or PowerPoint format.
Venue
The following page from the University's website helps you to find the campus but also gives hints on how to get to Bielefeld itself:
http://www.uni-bielefeld.de/%28en%29/Universitaet/Ueberblick/Anreise/
On Monday, we will be in the CeBiTec building - number 3 in the “Plan of the Campus”. On Tuesday, we will be in the tenth floor in part U of the main building - close to the “B” in “Universität Bielefeld (UHG)” in the “Plan of the Campus”. Take an elevator at M or V - some other elevators do not got up to the tenth floor (because there is no tenth floor everywhere).
Dinner (applicants and faculty only)
The Workshop Dinner on Monday will take place at Restaurant Bernstein. The following site is in German, but shows a picture of the building: http://www.bernstein-live.de/bernstein/anfahrt.html
On the backside of the building shown on the picture, you find the entrance to the restaurant. You have to take the elevator to the top level.
The Bernstein is next to “Jahnplatz”, which has an underground tram station. All lines stop here (if you choose the correct direction, of course). From the hotel, it it should be a 15-minutes walk If you get lost, just ask. Anybody in Bielefeld knows the “Jahnplatz” and most people speak English.
Hotel
All external applicants will stay at the B&B Hotel Bielefeld which is close to the main station. The way from the main station is described in this map.
Address: B&B Hotel Bielefeld, Europa Platz 2, 33613 Bielefeld
The rooms (including breakfast) are booked and will be payed directly by us.
The reception is not open 24/7. On Sundays, you can only enter the hotel for check-in or baggage drop-off from 7am to noon and from 5pm to 10pm. If you arrive later than 10pm, let us know and we organize a PIN code for you such that you can get into your room in the night.
Reimbursement
We assume that applicants arrive on Sunday and depart from Bielefeld on Wednesday. Please let us know the dates and times of your arrival and departure.
The hotel will be booked and payed by us.
Unfortunately, you will first have to pay everything else yourself (flight, train) and get reimbursed later, after the workshop.
You have to keep all receipts, boarding passes, tickets etc.! Please use economy flights and 2nd class train coaches.