Seren Soner, PhD
R&D Software Forensics Expert
@Quintiq Applications B.V

Utrecht, 2011

/summary/

currently i work in quintiq, where as an r&d software forensics expert, i aim to find the root causes of complex problems in quintiq's scp&o software or used 3rd party libraries. as part of my phd study, i've worked on optimization of job schedulers in heterogeneous systems with generic resources such as cpu and gpu or xeon phi. 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 my masters thesis, i had modeled the protein interactions using gaussian network model and wrote a scoring function to distinguish different interface types.

/education/

Sep 2009 - Jan 2016

Bogazici University, Computer Engineering Department, PhD
Thesis Title: Job scheduling for heterogeneous supercomputers Thesis Advisor: Prof. Dr. Can Ozturan various scheduling models have been proposed to solve the scheduling problem in heterogeneous supercomputers. these models are used to solve the online coallocation problem to find an optimal assignment of jobs in the queue to the available resources in the system. 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. GPA: 3.66

Sep 2007 - Jun 2009

Bogazici University, Chemical Engineering Department, MSc
Thesis Title: Study of protein-protein interfaces using Gaussian network model Thesis Advisor: Prof. Dr. Turkan Haliloglu distinction of protein interface types using gaussian network model into two classes: obligatory and non-obligatory. for the thesis project, a scoring function is written based on the properties obtained from different classes of proteins. a web server is made available to the bioinformatics community which uses this scoring function, and is available at http://safir.prc.boun.edu.tr/dynaface/. GPA: 3.75

Sep 2003 - Jun 2007

Bogazici University, Chemical Engineering Department, BSc
GPA: 3.38

Sep 1999 - Jun 2003

Kadikoy Anadolu Lisesi
GPA: 4.91

/publications/

  • DynaFace: Discrimination between obligatory and non-obligatory protein-protein interactions based on the complex’s dynamics
    Soner S., Ozbek P., Garzon JI., Ben-Tal N., Haliloglu T., PloS Computational Biology, Volume 11, 2015. doi: 10.1371/journal.pcbi.10044661
  • A new auction-based scheduler for heterogeneous systems with moldable generic resources support
    Soner S., Ozturan C., Concurrency and Computation: Practice and Experience, Volume 28, 2016, pages 2341-2352. doi: 10.1002/cpe.3653
  • Generating multibillion element unstructured meshes on distributed memory parallel machines
    Soner S., Ozturan C., Scientific Programming, 2015. doi: 10.1155/2015/437480
  • Integer Programming Based Heterogeneous CPU-GPU Cluster Schedulers for SLURM Resource Manager
    Soner S., Ozturan C., Journal of Computer and System Sciences, Volume 81, 2015, Pages 38-56. doi: 10.1016/j.jcss.2014.06.011
  • 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
  • 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/

Aug 2009 - Jul 2015

Research Assistant and System Administrator in Bogazici University, Polymer Research Center
- responsible for local cluster (384 cores) installation and management
- educated the researchers for efficient cluster usage
- project and grant application and follow ups

jun 2011

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

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