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Rasim Murat Aydınkal

You will find here the projects what I have done up to now as a computational biologist as well as my curriculum vitae.
I am currently having my PhD at the Marmara University, Department of Bioengineering.
You are very welcome to contact me if you wish to, via email, LinkedIn, Facebook or Skype.

Qualifications

  • Scientific Scripting
  • Structural Bioinformatics
  • Biodiversity Informatics
  • Web Apps via Relational Databases

Last Updates

I am going to attend to the World Flora Online Council meeting which will be held in St Louis, MO (USA).2019-Nov-10
I have a talk about the key features of Otobur in the Biodiversity_next conference in Leiden, The Netherlands.2019-Oct-02
Our last paper has been published in Nucleic Acids Research. ProSNEx is now online!2019-May-22
Trinity College Dublin (Ireland) is going to host the Council Meeting of the World Flora Online.2018-Dec-03
DUOF Herbarium (Duzce University) decided on selecting Otobur to manage their biodiversity data!2018-Nov-14
I am invited to share my experience in managing biodiversity data with Georgian colleagues at the National Botanical Garden of Georgia.2018-Oct-24

Education

PhD. Student, Bioengineering

Marmara University, Istanbul 2019 - Present

MSc., Bioengineering

Marmara University, Istanbul 2014 - 2019

MSc., Biology

Namik Kemal University, Tekirdag 2013 - 2016

BSc., Biology

Izzet Baysal University, Bolu 2007 - 2011

Awards

UNESCO

Cultural Challenge, Best Promotion 2005

Career

Head of Biodiversity Informatics

ANG Foundation, Istanbul 05 2012 - 07 2023

Bioinformatician

Epista Bioinformatics, Istanbul 09 2013 - 06 2022

Board Member

Aydınkal Group, Samsun 06 2022 - Present

Engineering Tool Skills

MATLAB

Programming Skills

Javascript & jQuery & Ajax

Node.JS

SQL

Bash Scripting

Perl

R

Python

ProSNEx

Protein Structure Network Explorer

Otobur™: Botanic Garden Data Management System

Turkish Patent and Trademark Office Grant No: 2017 17866
Web application system designed for collection management in botanical gardens, museums and historical societies.

Bağbahçe Science Journal

Supporting science journal in

- Database and Layout
- Server Management

BizimBitkiler

Web check-list of Turkish Flora.


Tehd!tAltinda

Web list of endangered species of Turkish plants.

SVN System

Subversion file/directory control system for illustrated flora of Turkey Project which is under Presidency of the Republic of Turkey.

e-Flora of Turkey

The first Turkish language account of Turkey's vascular plants as e-flora. turkiyeflorasi.org.tr

Herbarium Digitization

- Imaging
- Databasing
- Georeferencing

QR Code

QR code multimedia labels for public interpretation.

Article

Aydinkal, R.M., Sercinoglu, O., Ozbek, P. (2019)
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism, Nucleic Acids Research
doi: 10.1093/nar/gkz390

Aydinkal, R.M. and Bagci, E.Z., (2018)
Residue packing in globular and intrinsically disordered proteins. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.25459

Thesis

Computational investigation of the extent of regularities in residue packing in a representative group of intrinsically disordered proteins

Namik Kemal University, Tekirdag 2016

Development of a web–based tool for network analysis of protein structures

Marmara University, Istanbul 2019

Chapter in Book

Türkiye Bitkileri Listesi (Damarlı Bitkiler)

Nezahat Gökyiğit Botanik Bahçesi ve Flora Araştırmaları Derneği Yayını2012

Integrated Land-use Management Modelling of Black Sea Estuaries (ILMM-BSE) Project: Ergene River Basin

Namik Kemal University Press2016

Oral Presentation

Otobur™: Botanic Garden Data Management System

6th Global Botanic Gard. Cong., Geneva (Switzerland). doi: 10.5281/zenodo.11584312017

Otobur in Action

Biodiversity_next, Leiden (Netherlands).2019

Poster Presentation

Residue Packing at the Interfaces of Protein Complexes

5th Inter. BAU Drug Design Cong., Istanbul2017

Comparison of residue packing of housekeeping genes (GAPDH and UBQ- conjugat_E2) from human (Homo sapiens) and yeast (Saccharomyces cerevisiae) species with non-homologous globular proteins

1st Inter. Conf. of Genomics and Bioinformatics (ICGB), Aydın2018

Workshop Participant

Stereological Methods

Tur. Soc. for Stereology, Malatya (Turkey)2013

Linux Coding Summer Camp

Turkish Linux Users Association (LKD), Bolu2014

Molecular Modeling and Drug Discovery Technology

Acıbadem University, Istanbul (Turkey)2017

Dialogues in the MIDST: Residue Networks

Sabanci University, Istanbul (Turkey)2018

Workshop Organization

Otobur™: Complete Solution to the Data Management Challenges for Botanic Gardens

EUROGARD VIII, Lisbon (Portugal)2018

Scientific Community

International Society for Computational Biology

(2017-) Member

Congress Participant

22th National Biology Congress

Osmangazi University, Eskisehir (Turkey)2014

8th International Symposium on the Apiales

Istanbul University, Istanbul (Turkey)2015

National Plant Biology Congress

Izzet Baysal University, Bolu (Turkey)2015

Next Generation Pteridology

Smithsonian Inst., Washington DC. (U.S.A)2015

6th Global Botanic Gardens Congress

CJBG, Geneva (Switzerland)2017

5th International BAU Drug Design Congress

Istanbul (Turkey)2017

8th European Botanic Gardens Congress

Lisbon (Portugal)2018

Biodiversity_next Conference

Leiden (Netherlands)2019

Contact Me

Phone +90 (216) 456 4437

Cell +90 (535) 718 0719

Email a.rasimmurat@gmail.com

Website / Blog murataydinkal.com

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