Seren Soner, PhD
R&D Support Consultant
@Quintiq Applications B.V

Utrecht, 2011

/summary/

as a phd student in computer engineering, i've worked on optimization of job schedulers in heterogeneous systems with generic resources such as cpu and gpu or xeon phi. the aim is to improve the utilization of all the resources in the compute nodes, while minimizing the transfer cost between different nodes using topology awareness. i also participated in a project where we developed a tool in which multi billion element meshes can be generated in 8K cpu cores. in the past, i was also modeled the protein interactions using gaussian network model. currently i work in quintiq, where as an r&d support consultant, i aim to solve complex issues in an scp&o software.

/education/

Sep 2009 - Jan 2016

Bogazici University, Computer Engineering Department, PhD Student
GPA: 3.66

Sep 2007 - Jun 2009

Bogazici University, Chemical Engineering Department, MSc Student
Thesis Subject: Study of protein-protein interfaces using Gaussian network model Thesis Advisor: Prof. Dr. Türkan Haliloğlu GPA: 3.75

Sep 2003 - Jun 2007

Bogazici University, Chemical Engineering Department, BSc Student
GPA: 3.38

Sep 1999 - Jun 2003

Kadikoy Anadolu Lisesi
GPA: 4.91

/publications/

  • Integer Programming Based Heterogeneous CPU-GPU Cluster Schedulers for SLURM Resource Manager
    Soner S., Ozturan C., Journal of Computer and System Sciences, in press.
  • Hot Spots in a Network of Functional Sites
    Ozbek, P., Soner S., Haliloglu T., PloS one 8 (9), e74320 doi: 10.1371/journal.pone.0074320
  • Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
    Fleishman S.J, ..., Soner S., Ovali S.K, Ozbek P., Ben-Tal N., Haliloglu T., ..., Baker D., Journal of Molecular Biology, Volume 414, Issue 2, 25 November 2011, Pages 289-302 doi: 10.1016/j.jmb.2011.09.031
  • DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues
    Ozbek, P., Soner, S., Erman, B., Haliloglu, T., Nucleic Acids Research 2010; Web Server issue, 38:W417-423, 2010 doi: 10.1093/nar/gkq396

/prace whitepapers/

/conference presentations/

  • Integer Programming Based Heterogeneous CPU-GPU Cluster Scheduler for SLURM Resource Manager
    Soner S., Ozturan C., 2012 IEEE 14th International Conference on High Performance Computing and Communication & 2012 IEEE 9th International Conference on Embedded Software and Systems (HPCC-ICESS), 25-27 June 2012, pp.418-424 doi: 10.1109/HPCC.2012.63
  • Integer Programming Based Heterogeneous CPU-GPU Clusters, Soner, S., Ozturan C., SLURM User Group Meeting 2012, Barcelona, October 2012 link
  • Co-Allocation Based Scheduling For Parallel Systems (poster) Soner, S., Ozturan, C., Tosun, O. Supercomputing 2011, Seattle, WA, USA, 2011
  • Co-Allocation Based Scheduling For Parallel Systems (poster) Soner, S., Ozturan, C., Tosun, O. Supercomputing 2011, Seattle, WA, USA, 2011
  • Dynamics define protein binding (poster) Soner, S., Ozbek, P., Haliloglu, T., Chemical Physics Congress-IX Izmir, Turkey, 2010
  • Dynamics and evolutionary conservation of inter-protein interfaces aid in the detection of native complexes amongst docking decoys (poster) Ozbek, P., Soner, S., Chen, N., Kalman, M., Erman, B., Ben-tal, N., Haliloglu, T., 4th CAPRI meeting, Barcelona, 2009

/work experience/

jun 2011

Three-days workshop on HADDOCK
member of organization committee
Istanbul, Boğaziçi University, 20-22 June 2011

Aug 2009 -

Research Assistant and System Administrator in Bogazici University, Polymer Research Center

Sep 2007 - Jul 2009

Teaching Assistant in Bogazici University, Chemical Engineering Department
Assisted courses:
- ChE 321: Chemical Engineering Thermodynamics
- ChE 310: Introduction to Macromolecular Systems
- ChE 598: Special Topic: Probabilistic Models of Proteins
- ChE 460: Total Quality Engineering in Chemical Industries

/projects/

2013 - 2014

FP7 PRACE 3IP project grant number : RI-312763
- Subtask 7.2 Researcher. PI: Assoc. Prof. Can Özturan

2012 - 2014

FP7 PRACE 2IP project grant number : FP7-283493
- Subtask 12.1 Researcher. PI: Assoc. Prof. Can Özturan

2010 - 2012

FP7 PRACE 1IP project grant number : RI-261557
- Subtask 9.2.C Researcher. PI: Assoc. Prof. Can Özturan

2009 - 2011

“Protein-Protein Etkileşim Arayüzlerinin Dinamik Karakterizasyonu” (Dynamic Characterisation of Protein-Protein Interfaces), Bogazici University Research Fund Project
Researcher. PI: Prof. Türkan Haliloğlu