Open PhD positions on High-Performance Brain Simulations

 

Reference number: REF 216

Our Computer Engineering group of the Neuroscience Department of the Erasmus Medical Center, the Netherlands, in conjunction with the Computer-Engineering and Embedded-Systems groups of the Delft University of Technology is conducting research on next-generation, high-performance, large-scale simulations of the human cerebellum. Depending on the neuronal-network size and the modeling accuracy desired, brain-model simulations can rapidly grow to be become exascale order-of-magnitude applications for HPC platforms. By capitalizing on the long-standing expertise and track record of the Neuroscience Department, the overall objective of the research performed is dual: to re-construct in hardware (‘in silico’) the human cerebellar cortex and – in the process – to develop novel tools for the automatic, seamless and fast simulation of any brain-model ensembles on popular HPC platforms, such as FPGAs, NVidia GP-GPUs, Intel Xeon Phis and Maxeler Dataflow Engines. The selected candidates are expected to work on these topics.

 

The research group has a solid track record in contributing to design principles of high-performance and low-power embedded computing systems. Erasmus MC is a partner in the HiPEAC European Network of Excellence and an official collaborator in the H2020 Flagship: Human Brain Project (HBP - www.humanbrainproject.eu). Where HBP works on fully simulating the cerebral cortex, Erasmus MC is adding in accurate simulations of the cerebellar cortex.

 

This research will be part of the VINEYARD Horizon 2020 EU-funded project (www.vineyard-h2020.eu). Collaborative partners are the Chalmers University of Technology and the National Technical University of Athens.

 

Job description:

The United States National Academy of Engineers has classified brain emulation as one of the Grand Engineering Challenges. Brain emulation in-silico is a relevant research field for various reasons such as accelerated brain exploration and brain rescue. The short term goal of the project is to apply high-performance solutions to accelerate and enable large-scale, accurate brain simulations or enhance data analysis of the experimental data concerning brain research. The long term goal of this effort is the development of a generic tooling framework for accelerated brain simulations. As part of our ongoing work on high-performance brain simulations and of our participation in the VINEYARD project (and the HBP Flagship), we are recruiting one PhD student to work on the following topics:

  • Efficient parallelization and porting of existing high-detail brain models (extended Hodgin-Huxley, adaptive exponential etc.) to cutting-edge, HPC parallel platforms (e.g. Maxeler Dataflow Engines).
  • Extension of existing toolflow for automatically porting and simulating various neuron models from an official HBP Python front-end (PyNN) to a multi-node HPC parallel platform.
  • Co-development of proof-of-concept Brain-Machine Interface (BMI) for rescuing parts of a damaged cerebellum on live animals.

All above topics will be supported by various specialists in the Neuroscience Department, e.g. neuron models will be provided based on clinical animal experiments, Machine interfaces will be provided as-is etc.

 

More information about the research theme is available at:

 

Required qualifications:

PhD applicants shall have a Master’s Degree or equivalent in Computer Engineering or in a related discipline. A genuine interest and curiosity in the subject matter and excellent analytical and communication skills in speaking and in writing are required. Furthermore, since the research work normally involves developing simulation models of detailed processor/system architectures and hardware designs, good programming skills as well as good hardware design skills are important. Prior experience with high-performance scientific computing (especially neuroscience) or with source-to-source translation and tool design are considered a plus, although not mandatory. Successful candidates will have a profound interest in computer architectures and a foundation in hardware design.

 

As a PhD student, you will be employed by Erasmus Medical Center and will receive a salary according to current salary agreements. A maximum of 20% of your time will be devoted to other duties than your PhD studies, mainly student-thesis supervision and teaching. The remaining time will be devoted to your own PhD research, and you are expected to obtain a Ph.D. within 4 years. Adjustments to this timeframe will be considered per case.

 

Application details:

It is highly recommended that you include or e-mail at least 2 letters of recommendation: we typically get many applications, and it is simply not feasible for us to request individual letters.

 

It is essential that the application includes all relevant work such as theses and articles that you have authored or co-authored.

 

Application procedure:

The application shall be written in English and include the following items:

 

   1. An application of a maximum of one A4 page containing your specific qualifications for the position

   2. Attested copies of education certificates, including grade reports and other documents

   3. Curriculum Vitae

   4. Letters of recommendation and name of reference persons (optional)

 

The application shall be sent electronically as pdf or zipped documents. Please direct all questions and send all correspondence materials to: This email address is being protected from spambots. You need JavaScript enabled to view it. .

 

If any material is not available electronically or cannot be transferred to pdf format, the material can be sent as a hard copy to our coordinator Ms. Buitenhuis-Linssen (Attention: Christos Strydis). The applicant’s name and the reference number (REF 216) must be written on the first page of the application.

 

Address:

Elise Buitenhuis-Linssen

Coordinator Department of Neuroscience

Erasmus Medical Center

P.O. Box 2040

3000 CA Rotterdam

The Netherlands

 

Further information:

Research level:

Assistant Professor Christos Strydis

Wytemaweg 80 (12th floor)

Office Ee1210a

3015 CN Rotterdam

The Netherlands

Web: www.erasmusbrainproject.com/index.php/strydis

Tel: +31 107043294

Fax: +31 107044734

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Departmental level:

Chair Professor Chris I. de Zeeuw

Tel: +31 0107043299

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 


Open PhD positions on Secure and Fault-Tolerant Implant Architectures [FILLED]

 

Reference number: REF 116

Our Computer Engineering group of the Neuroscience Department of the Erasmus Medical Center, the Netherlands, in conjunction with the Computer-Engineering and Embedded-Systems groups of the Delft University of Technology is conducting research on next-generation implantable medical devices (IMDs). IMDs are resource-constrained embedded systems with unique functional and quality requirements. The overall objective of the research performed is to deliver techniques at the implant architecture, compiler, system and communication level for achieving by-design IMD security, privacy and fault tolerance. The selected candidates are expected to work on one or more of these intertwining subjects.

 

The research group has a solid track record in contributing to design principles of high-performance and low-power embedded computing systems. Erasmus MC is a partner in the HiPEAC European Network of Excellence and in the SINS consortium (http://www.braininnovations.nl/engels.php).

 

This research will be part of the SHARCS Horizon 2020 EU-funded project (www.sharcs-project.eu). Collaborative partners are the Chalmers University of Technology and the National Technical University of Athens.

 

Job description:

IMDs are a class of embedded systems which, on one hand, are highly constrained in terms of resources (performance, energy, area), yet they are also life-critical and should operate in a robust manner over extended periods of time (e.g. a decade or more). Subject to strict low-power and reliability requirements, modern implants have recently been retrofitted with wireless-communication capabilities effectively becoming smart cyberphysical systems (S-CPS) for medical contexts. As such, they now also pose strict requirements on security and privacy, both aspects where current implants are found seriously lacking.

 

As part of our long-standing work on IMD design and of our participation in the SHARCS project, we are recruiting one PhD student and one PostDoctoral researcher to work on the following topics:

  • Hardware/software techniques for security, privacy and fault tolerance at the IMD architecture, interconnect and system level;
  • Energy-harvesting-based, hardware/software techniques for secure IMD communication;
  • Cutting-edge, new IMD applications such as seizure-prevention neural implants.

The rest of the traditional aspects of implant design (such as low power and energy consumption, small memory footprint, small chip area) will also be considered.

 

More information about the research theme is available at:

 

Required qualifications:

PhD applicants shall have a Master’s Degree or equivalent in Computer Engineering or in a related discipline. A genuine interest and curiosity in the subject matter and excellent analytical and communication skills in speaking and in writing are required. Furthermore, since the research work normally involves developing simulation models of detailed processor/system architectures and hardware designs, good programming skills as well as good hardware design skills are important. Prior experience with cryptographic algorithms, security protocols, fault-tolerant design are considered a plus, although not mandatory. Successful candidates will have a profound interest in computer architectures and a foundation in hardware design.

 

As a PhD student, you will be employed by Erasmus Medical Center and will receive a salary according to current salary agreements. A maximum of 20% of your time will be devoted to other duties than your PhD studies, mainly student-thesis supervision and teaching. The remaining time will be devoted to your own PhD research, and you are expected to obtain a Ph.D. within 4 years. Adjustments to this timeframe will be considered per case.

 

Application details:

It is highly recommended that you include or e-mail at least 2 letters of recommendation: we typically get a large number of applications, and it is simply not feasible for us to request individual letters.

 

It is essential that the application includes all relevant work such as theses and articles that you have authored or co-authored.

 

Application procedure:

The application shall be written in English and include the following items:

 

   1. An application of a maximum of one A4 page containing your specific qualifications for the position

   2. Attested copies of education certificates, including grade reports and other documents

   3. Curriculum Vitae

   4. Letters of recommendation and name of reference persons (optional)

 

The application shall be sent electronically as pdf or zipped documents. Please direct all questions and send all correspondence materials to: This email address is being protected from spambots. You need JavaScript enabled to view it. .

 

If any material is not available electronically or cannot be transferred to pdf format, the material can be sent as a hard copy to our coordinator Ms. Buitenhuis-Linssen (Attention: Christos Strydis). The applicant’s name and the reference number (REF 116) must be written on the first page of the application.

 

Address:

Elise Buitenhuis-Linssen

Coordinator Department of Neuroscience

Erasmus Medical Center

P.O. Box 2040

3000 CA Rotterdam

The Netherlands

 

Further information:

Research level:

Assistant Professor Christos Strydis

Wytemaweg 80 (12th floor)

Office Ee1210a

3015 CN Rotterdam

The Netherlands

Web: www.erasmusbrainproject.com/index.php/strydis

Tel: +31 107043294

Fax: +31 107044734

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Departmental level:

Chair Professor Chris I. de Zeeuw

Tel: +31 0107043299

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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