A. Anil Sinaci

I am a software engineer and computer scientist with 15+ years of development experience ranging from desktop, web and mobile applications to cutting-edge research projects. I am a principal software engineering manager and senior researcher at SRDC Corp. I make hiring decisions, build and manage teams, lead engineering decisions, and deliver software: products and services for customers, and solutions for research projects. I work as a part-time instructor at METU-CENG.

I hold a PhD in computer science/engineering since 2014. I actively worked for many large-scale, international R&D projects at different stages such as creating ideas/innovation, compiling the project proposals, designing and implementing the solutions, and leading/managing scientific and technical teams. I authored many papers published in peer-reviewed journals and conferences.

I contribute to open-source software development, I became an Apache committer with the (retired) Apache Stanbol project. I maintain the source codes of the research projects that I lead on GitHub. I contribute to standardization activities. In the past, I worked as a member of the technical and planning committees of IHE QRPH. I am the leading editor of the ISO/IEC DEX standard.

My research areas

Data Management

Relational, graph and document databases. Indexing, query planning/optimization and query processing. Distributed data processing and sharding. ETL architectures and domain-specific data transformation. Semantic indexing and semantic search mechanisms on content management systems.

Interoperability

Service Oriented Architectures (SOA). Domain-specific interoperability solutions, interoperability standards, conformance and interoperability testing. Metadata registries, Common Data Elements, syntactic and semantic mappings. Findable, Accessible, Interoperable, Reusable (FAIR) principles.

Semantic Web & Linked Data

Named entity recognition, knowledge representation and entity linking. Semantic modeling, semantic interoperability and graph query processing. Semantic data management and triple-stores. Inference engines (reasoners) and recommendation systems.

Machine Learning

Descriptive and prescriptive statistics. Statistical inference, artificial neural networks. Federated machine learning. Distributed data mining. Privacy-preserving machine learning. Artificial intelligence in healthcare and clinical research.

Big Data Analytics & Business Intelligence

Big data technology stack. Customized big data infrastructures. Distributed big data processing. Data cleaning, transformation and information/meaning extraction. Predictive and prescriptive analytic solutions with data visualization for informed decisions.

eHealth Infrastructures

Clinical decision support systems. Automated clinical guidelines. Health data interoperability. Secondary use of healthcare data, clinical research informatics & biomedical informatics. Practical applications of artificial intelligence in health.

Education

A lifelong learner
2009 - 2014
Middle East Technical University, Ankara, Turkey

Ph.D. in Computer Engineering

The title of my PhD dissertation is Data Interoperability Through Federated Semantic Metadata Registries. During my PhD studies, I designed and implemented a novel interoperability architecture based on the concept of Common Data Elements while utilizing the semantic web technologies and Linked Data principles.

Data interoperability is a hindering challenge for many domains as such in eHealth and eBusiness applications where valuable data is kept in different silos and applications try to make use of those disparate datasets for various use-cases. Associated IT communities are trying to find new ways for interoperability and publishing domain-specific Common Data Elements is one of those abstract solutions to alleviate the pain: defining abstract metadata definitions for data items to be exchanged or collaboratively processed. I proposed a solution for this problem of data interoperability based on federated use of metadata registries utilizing Semantic Web and Linked Data technologies. My related publication received 67 citations so far.

I pursued my work under great coordination of my lovely supervisor, Prof. Dr. Nihan Kesim Cicekli. My studies led to the development of a new profile, named Data Element Exchange, under Integrating the Healthcare Enterprise. Later on, based on this idea, I co-authored a new ISO/IEC standard.

2007 - 2009
Middle East Technical University, Ankara, Turkey

MSc. in Computer Engineering

The title of my MSc thesis is A Conformance and Interoperability Test Suite For Turkey's National Health Information System and An Interactive Test Control and Monitoring Environment. The first version of Turkey's National Health Information System (NHIS) was based on HL7 standards. Clients such as the hospital information systems continuously submitted medical data through this system to the central web services. During my masters studies, I built a testing environment so that the clients can test themselves in terms of conformance and interoperability with respect to the standards used in various layers of the web service communication.

2003 - 2007
Middle East Technical University, Ankara, Turkey

BSc. in Computer Engineering

During my undergraduate education, in addition to the core/must courses of the department on Data Structures, Algorithms, Programming Language Concepts, Operating Systems etc., I took several technical elective courses such as Artificial Intelligence, Language Processors, Database Management Systems and Introduction to Bioinformatics. I will always remember the programming assignments, group projects and long and sleepless nights at the laboratories.

1996 - 2003
Icel Anatolian High School, Mersin, Turkey

High School - Science Diploma

From age 11 to 18, more than 7 years at the beautiful campus of my high school by the sea side. Lots of memories, I grew up there...

Experience

15 years of experience
2011 - Current
SRDC Software Research & Development and Consultancy Corporation, Ankara, Turkey

Principal Software Engineering Manager, Senior Researcher

SRDC turned into a successful, R&D oriented tech company. Growing together with the company, I sharpened my skills by continously learning from many challenging tasks.

2016 - 2020
Department of Computer Engineering, Middle East Technical University, Ankara, Turkey

Instructor

Alongside my full-time job at SRDC, I worked as a course instructor at the Department of Computer Engineering offering the following courses:

Here is a slide deck that I prepared for one lesson of Ceng 229 from Fall 2018:

2009 - 2011
Department of Computer Engineering, Middle East Technical University, Ankara, Turkey

Teaching Assistant

During the 2 years (4 semesters) at the Department of Computer Engineering, I worked as a teaching assistant; lectured the laboratory sessions and recitations, and prepared and evaluated many programming assignments.

Here are two programming assignments that I prepared for the undergraduate students:

Here is the list of the courses that I worked for:

2010 - 2011
Cengsoft, Ankara, Turkey

R&D Consultant

While I was a teaching assistant at the Department of Computer Engineering, I worked as a technical consultant to support the product development of CengSOFT Ltd. (later, became a part of SOMERA). We used Apache Struts to build a web application and I mainly took part in the back-end development.

2009 - 2010
AGMLab Information Technologies, Ankara, Turkey

R&D Consultant

While I was a teaching assistant at the Department of Computer Engineering, I worked as an academic R&D consultant to support AGMLab's international research project called SEMbySEM. I contributed to the arhictecture design and semantic modeling of large system services and their dynamic integration to support interoperability of services on the fly.

2007 - 2009
Software Research Development Center, Middle East Technical University, Ankara, Turkey

Software Engineer, Researcher

After graduation, I started working as a full-time software engineer at SRDC. I had the chance of being a key member of the TestBATN project where I designed the API, developed its back-end and the web front-end so that the end-users can interact with the testing engine. I implemented various networking standards in the back-end, and developed a rich internet application with Adobe Flex (Apache Flex) which was very exciting back then 😉 I remember that after very long discussions, we even implemented our own version of WebSocket using Adobe Flash. My first full-time job was extremely educational and pragmatic for me.

2006 - 2007
Software Research Development Center, Middle East Technical University, Ankara, Turkey

Part-time Software Developer

After successfully completing my summer practice at SRDC, I was offered a part-time job. I worked as a software developer to support the ongoing R&D projects which were mainly on service-oriented architectures, peer-to-peer communication and databases.

Portfolio

My Works
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AICCELERATE

Artificial Intelligence, Big Data Management, Data transformation, eHealth, ETL (Extract-Transform-Load), FAIR, Interoperability, Machine Learning
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FAIR4Health

Artificial Intelligence, eHealth, FAIR, Machine Learning
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Weather Forecast App for Turkey

Data transformation, ETL (Extract-Transform-Load), Mobile Development
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SALUS

Data transformation, Data/Metadata standardization, eHealth, Interoperability, Semantic Web
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mantIQ – Business Intelligence

Artificial Intelligence, Big Data Management, Data transformation, eBusiness, ETL (Extract-Transform-Load)
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onFHIR

Big Data Management, Data/Metadata standardization, eHealth, Interoperability
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Federated Machine Learning

Artificial Intelligence, Machine Learning
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Data Privacy Tool

Data security/privacy, Data transformation, eHealth
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Semantic MDR

Data transformation, Data/Metadata standardization, eBusiness, FAIR, Interoperability
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Apache Stanbol

Data transformation, Data/Metadata standardization, Interoperability, Semantic Web
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Data Curation Tool

Data transformation, Data/Metadata standardization, eHealth, ETL (Extract-Transform-Load), FAIR
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Medolution

Big Data Management, Data transformation, eHealth
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Arrays & Pointers

Teaching
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BIVEE

Business Innovation, Data transformation, eBusiness, ETL (Extract-Transform-Load)
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Interactive Knowledge Stack

Big Data Management, Data transformation, Interoperability, Semantic Web
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TestBATN

eHealth, Interoperability
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Escape From Shawshank

Teaching
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(Modified) Linear Hashing with Partial Expansions

Teaching

Publications

I do research

Peer-reviewed Journal Publications

A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains

Sinaci AA, Erturkmen GB.
A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.
Journal of biomedical informatics. 2013 Oct 1;46(5):784-94.
Total number of citations: 67

A semantic backend for content management systems

Laleci GB, Aluc G, Dogac A, Sinaci AA, Kilic O, Tuncer F.
A semantic backend for content management systems.
Knowledge-based systems. 2010 Dec 1;23(8):832-43.
Total number of citations: 43

From Raw Data to FAIR Data: The FAIRification Workflow for Health Research

Sinaci AA, NĂșñez-Benjumea FJ, Gencturk M, Jauer ML, Deserno T, Chronaki C, Cangioli G, Cavero-Barca C, RodrĂ­guez-PĂ©rez JM, PĂ©rez-PĂ©rez MM, Laleci Erturkmen GB, HernĂĄndez-PĂ©rez T, MĂ©ndez-RodrĂ­guez E, Parra-CalderĂłn CL.
From Raw Data to FAIR Data: The FAIRification Workflow for Health Research.
Methods Inf Med. 2020 Jun;59(S 01):e21-e32. doi: 10.1055/s-0040-1713684. Epub 2020 Jul 3. PMID: 32620019.
Total number of citations: 26

A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies

Pacaci A, Gonul S, Sinaci AA, Yuksel M, Laleci Erturkmen GB.
A semantic transformation methodology for the secondary use of observational healthcare data in postmarketing safety studies.
Frontiers in pharmacology. 2018 Apr 30;9:435.
Total number of citations: 13

An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies

Yuksel M, Gonul S, Laleci Erturkmen GB, Sinaci AA, Invernizzi P, Facchinetti S, Migliavacca A, Bergvall T, Depraetere K, De Roo J.
An interoperability platform enabling reuse of electronic health records for signal verification studies.
BioMed research international. 2016 Oct;2016.
Total number of citations: 10

Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance Studies

Sinaci AA, Laleci Erturkmen GB, Gonul S, Yuksel M, Invernizzi P, Thakrar B, Pacaci A, Cinar HA, Cicekli NK.
Postmarketing safety study tool: a web based, dynamic, and interoperable system for postmarketing drug surveillance studies.
BioMed research international. 2015 Jan 1;2015.

Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm

Carmona-PĂ­rez J, Poblador-Plou B, Poncel-FalcĂł A, Rochat J, Alvarez-Romero C, MartĂ­nez-GarcĂ­a A, Angioletti C, Almada M, Gencturk M, Sinaci AA, Ternero-Vega JE, Gaudet-Blavignac C, Lovis C, Liperoti R, Costa E, Parra-CalderĂłn CL, Moreno-Juste A, Gimeno-Miguel A, Prados-Torres A.
Applying the FAIR4Health Solution to Identify Multimorbidity Patterns and Their Association with Mortality through a Frequent Pattern Growth Association Algorithm.
International Journal of Environmental Research and Public Health. 2022; 19(4):2040. https://doi.org/10.3390/ijerph19042040

Predicting 30-days Readmission Risk for COPD Patients Care through a Federated Machine Learning Architecture on FAIR Data: Development and Validation Study

Alvarez-Romero C, MartĂ­nez-GarcĂ­a A, Ternero-Vega JE, Diaz-Jimenez P, Jimenez-De-Juan C, Nieto-Martin MD, Roman-Villaran E, Kovacevic T, Bokan D, Hromis S, Djekic Malbasa J, Beslac S, Zaric B, Gencturk M, Sinaci AA, Ollero-Baturone M, Parra-CalderĂłn CL.
Predicting 30-Day Readmission Risk for Patients With Chronic Obstructive Pulmonary Disease Through a Federated Machine Learning Architecture on Findable, Accessible, Interoperable, and Reusable (FAIR) Data: Development and Validation Study.
JMIR Medical Informatics. 21/04/2022:35307 (forthcoming/in press). http://dx.doi.org/10.2196/35307

Peer-reviewed Conference Publications

A Framework for Evaluating and Utilizing Medical Terminology Mappings

Hussain S, Sun H, Sinaci AA, Erturkmen GB, Mead C, Gray AJ, McGuinness DL, Prud'Hommeaux E, Daniel C, Forsberg K.
A framework for evaluating and utilizing medical terminology mappings.
Stud Health Technol Inform. 2014;205:594-8. PMID: 25160255.
Total number of citations: 10

Testing the Conformance and Interoperability of NHIS to Turkey’s HL7 Profile

Namli T, Aluc G, Sinaci AA, Kose I, Akpinar N, Gurel M, Arslan Y, Ozer H, Yurt N, Kirici S, Sabur E.
Testing the Conformance and Interoperability of NHIS to Turkey’s HL7 Profile.
9th International HL7 Interoperability Conference [Internet]. Crete, Greece 2008 Oct (pp. 63-8).
Total number of citations: 10

Optimization of just-in-time adaptive interventions using reinforcement learning

Gonul S, Namli T, Baskaya M, Sinaci AA, Cosar A, Toroslu IH.
Optimization of just-in-time adaptive interventions using reinforcement learning.
International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems 2018 Jun 25 (pp. 334-341). Springer, Cham.
Total number of citations: 9

Standard-based EHR-enabled applications for clinical research and patient safety: CDISC -- IHE QRPH -- EHR4CR & SALUS collaboration

Daniel C, Erturkmen GB, Sinaci AA, Delaney BC, Curcin V, Bain L.
Standard-based integration profiles for clinical research and patient safety.
AMIA Jt Summits Transl Sci Proc. 2013;2013:47-49. Published 2013 Mar 18.
Total number of citations: 7

Standard-based integration profiles for clinical research and patient safety

Daniel C, Erturkmen GB, Sinaci AA, Delaney BC, Curcin V, Bain L.
Standard-based integration profiles for clinical research and patient safety.
AMIA Summits on Translational Science Proceedings. 2013;2013:47.
Total number of citations: 5

A Document Centric Approach for User Requirements in BIVEE

Sinaci AA, Piersantelli M, Cristalli C, Gigante F, Erturkmen GB, Basar RV.
A Document Centric Approach for User Requirements in BIVEE.
CAiSE Conference, Workshop on New Generation Enterprise and Business Innovation Systems, June, 2012, Gdansk, Poland.
Total number of citations: 5

End User Evaluation of the FAIR4Health Data Curation Tool

Gencturk M, Teoman A, Alvarez-Romero C, Martinez-Garcia A, Parra-Calderon CL, Poblador-Plou B, Löbe M, Sinaci AA.
End User Evaluation of the FAIR4Health Data Curation Tool.
Studies in health technology and informatics. 2021 May 27;281:8-12.

FAIR4Health FAIRification Tools

Alvarez-Romero C, Martinez-Garcia A, Gencturk M, Sinaci AA, Parra-Calderon CL.
FAIR4Health FAIRification Tools.
Studies in health technology and informatics. 2021 May 27;281:8-12.

Transforming Health Data into Timeseries for Predictive Analytics

Sinaci AA, Namli T, Postaci S, Gencturk M, Erturkmen GB.
End User Evaluation of the FAIR4Health Data Curation Tool.
Studies in health technology and informatics. 2021 May 27;281:8-12.

The Health Data Ingestion Stack

Erturkmen GB, Sinaci AA, Namli T.
The Health Data Ingestion Stack.
Informatics for Health 2017, April, 2017, Manchester, UK

keyCRF: Using Semantic Metadata Registries to Populate an eCRF with EHR Data

Erturkmen GB, Bain L, Sinaci AA.
keyCRF: Using Semantic Metadata Registries to Populate an eCRF with EHR Data.
International Semantic Web Conference (Industry Track) 2014.

Adverse Drug Event Notification on a Semantic Interoperability Framework

Krahn T, Eichelberg M, MĂŒller F, GönĂŒl S, Laleci Erturkmen GB, Sinaci AA, Appelrath HJ.
Adverse drug event notification on a semantic interoperability framework.
Stud Health Technol Inform. 2014;205:111-5. PMID: 25160156.

Patient History Navigation with the Use of Common Data Elements

Sinaci AA, Erturkmen GB, GönĂŒl S, Cinar HA, Kaya A.
Patient History Navigation with the Use of Common Data Elements.
SWAT4LS 2013.

Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization Studies

Yuksel M, GönĂŒl S, Erturkmen GB, Sinaci AA, Depraetere K, De Roo J, Bergvall T.
Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization Studies.
SWAT4LS 2013.

Analysis of the Information Resources for the Furniture Industry in BIVEE

Gigante F, CrespĂ­ P, Sinaci AA, Basar RV.
Analysis of the Information Resources for the Furniture Industry in BIVEE.
NGEBIS Short Papers 2013 (pp. 1-6).

Semantic UBL-like documents for innovation

Basar RV, Sinaci AA, Smith F, Taglino F.
Semantic UBL-like documents for innovation.
NGEBIS Short Papers 2013 (pp. 39-44).

Semantic-sensitive extraction of EHR data to support adverse drug event reporting

Declerck G, Hussain S, ParĂšs Y, Daniel C, Jaulent MC, Yuksel M, Sinaci AA, Erturkmen GB.
Semantic-sensitive Extraction of EHR data to Support Adverse Drug Event Reporting.
SWAT4LS 2012.

Jena based Implementation of a ISO 11179 Metadata Registry

Sinaci AA.
Jena based Implementation of a ISO 11179 Metadata Registry.
ApacheCon, Sinsheim, Germany, 2012.

Semantic Content Management and Integration with JCR/CMIS Compliant Content Repositories

Gonul S, Sinaci AA.
Semantic Content Management and Integration with JCR/CMIS Compliant Content Repositories.
I-Semantics Conference, September, 2012, Graz, Austria

Semantic Content Management with Apache Stanbol

Sinaci AA, Gonul S.
Semantic Content Management with Apache Stanbol.
ESWC Conference, May, 2012, Heraklion, Crete, Greece

Building the Semantic Interoperability Architecture Enabling Sustainable Proactive Post Market Safety Studies

Erturkmen GB, Dogac A, Yuksel M, Hussain S, Declerck G, Daniel C, Sun H, Depraetere K, Colaert D, Devlies J, Krahn T, Thakrar B, Freriks G, Bergvall T, Sinaci AA.
Building the Semantic Interoperability Architecture Enabling Sustainable Proactive Post Market Safety Studies.
SIMI Workshop (Semantic Interoperability in Medical Informatics), in ESCW 2012: Extended Semantic Web Conference, May, 2012, Heraklion, Crete, Greece.

A semantically Enriched Persistence Mechanism for Interactive Knowledge Stack

Dogac A., Laleci G. B., Aluc G., Sinaci AA., Behrendt W., Delacretaz B., Pittet J. M.
A semantically Enriched Persistence Mechanism for Interactive Knowledge Stack.
eChallenges Conference, October, 2009, Istanbul, Turkey

Testing the Interoperability and Conformance of UBL/NES based Applications

Namli T, Dogac A, Sinaci AA, Aluc G.
Testing the Interoperability and Conformance of UBL/NES based Applications.
eChallenges Conference, October, 2009, Istanbul, Turkey

Book Chapters

Innovation and Production Improvement in Virtual Enterprises: The User Perspective

Pacaci A, Sinaci AA, Dogac A.
Innovation and Production Improvement in Virtual Enterprises: The User Perspective.
Enterprise Innovation: From Creativity to Engineering. 2015 Aug 20:233-56.

A Day of Networked Production Improvement

Valencia FG, Pacaci A, Sinaci AA.
A Day of Networked Production Improvement.
Enterprise Innovation 2015 Aug 7.

Standards & Profiles

Information technology — Concepts and usage of metadata — Part 23: Data element exchange (DEX) for a subset of ISO/IEC 11179-3

Erturkmen GB, Sinaci AA.
Information technology — Concepts and usage of metadata — Part 23: Data element exchange (DEX) for a subset of ISO/IEC 11179-3.
ISO/IEC TR 19583-23:2020

Data Element Exchange (DEX) Interoperability Profile

Bain L, Erturkmen GB, Daniel C, Sinaci AA.
Data Element Exchange (DEX) Interoperability Profile.
Technical report, IHE Quality, Research and Public Health Domain (QRPH) Technical Framework, September, 2013

Dissertations

Data Interoperability through Federated Semantic Metadata Registries

Sinaci AA.
Data Interoperability through Federated Semantic Metadata Registries.
PhD Dissertation, Middle East Technical University, Turkey, July 2014.

A Conformance and Interoperability Test Suite for Turkey’s NHIS and An Interactive Test Control and Monitoring Environment

Sinaci AA.
A Conformance and Interoperability Test Suite for Turkey’s NHIS and An Interactive Test Control and Monitoring Environment.
MSc. Dissertation, Middle East Technical University, Turkey, June 2009.

Others

User scenarios to promote the use of FAIR data on health research

Almada M, Dias I, Portela D, MidĂŁo L, Sinaci AA, NĂșñez-Benjumea FJ, Parra-CalderĂłn CL, Costa E.
User scenarios to promote the use of FAIR data on health research.
Open Science Fair, September, 2019, Porto, Portugal

Mountaineering

I love outdoor activities

I have always be in sportive activities since my childhood. During my universtiy years, I became a fond of outdoor sports when I attended the Mountaineering and Winter Sports Club. Along with a very well-formulated theoretical and practical education on mountaineering, I went to many camping activity and climbed several mountains in Turkey.

Below, I put some pictures of mine from the lovely Aladaglar which can be considered as the temple of mountaineering in Turkey.

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I am a member of the Middle East Search-Rescue, Mountaineering, and Outdoor Sports Association (ORDOS) which was founded in 1994 by the alumni of Middle East Technical University Mountaineering and Winter Sports Club. I served in the board of ORDOS for 4 years and I was the president for 2 years.

As ORDOS, since 2015, we organize the Aladaglar Skytrail trail run on diffrerent routes. Aladaglar Skytrail provides ITRA accredited trail races. I served in the race preparation committee for 2 years where I acted as technical coordinator and race coordinator, consecutively. I put two pictures below where I wish luck to my brother who was a runner at Skytrail and giving the awards to the winners. More pictures can be found on the Instagram of Aladaglar Skytrail.

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Contact

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