Hi, my name is David Aragão

I am a protein crystallographer, a beamline scientist, a linux Sys Admin and programmer.
I am also a proud father and uncle of future generation human beings.

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About Me

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Hi, my name is David Aragão

My main interests are structural biology, synchrotrons with its related beamline science, linux administration and using programming as a tool to improve research experiments.

Name: David Aragão

Phone: (+44) 01 865600998 

Email: david.aragao@cientistas.net

Address: Oxfordshire, UK

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My Experience

Protein Crystallographer
1998-2020
From 1998 a regular users of MX beamlines at more than 5 synchrotrons worldwide with over 10,000 hours collecting data and > 63 structures in the PDB have extensive experience in crystallisation, harvesting crystals, data collection, data reduction, structural solution, refinement and structural analysis of proteins structures.  Have over 35 peer-review publications having collected > 1,500 citations from 2003. 

Major achivements
  • Involvement in membrane protein work on GPCRs that led to the award of the Nobel Prize in Chemistry to Prof Brian Kobila 
  • Shining light into the electron transfer between cytochrome c and respiratory complex IV. This is part of one of the most important energy generation processes in celular life. 
  • Understanding a membrane kinase in incredible detail using both synchrotron and XFEL radiation. 
  • Proving that small membrane peptides could be solved by crystallography using lipidic cubic phase
Linux System Administrator
1995-2020
Started with SGI UNIX flavour IRIX rapidily gained experience installing and configuring Linux operating systems. Initially with paid jobs to setup computers for undergraduate chemical enginnering classes (SUSE Linux) but later to setup and administer RedHat, Debian and Slackware LAMP servers. Keen supported of Free Software and Open Source is a proud member of the Free Software Fundation since 2003

Free Software Foundation



System administrator of 3 Virtual Private Servers (VPS) hosting more than 60 domain names since 2003 gave him extensive experience in cPanel/WHM hosting, troubleshooting operating systems, investigation breaches and closing insecurity from Apache webservers, EXIM email servers, DNS servers, Firewall, etc. 

Attended and passed the demanding RH exams for:
  • 2013 - Certified Engineer (RHCE)
  • 2012 - Certified System Administrator (RHCSA)
Having been the de facto local System Administrator for the two Australian Synchrotron MX beamlines from 2012 to 2019. Here gained extenstive experience with virtual machines and linux kernel containers namely using the open source Proxmox Cluster software. Led the replacement of all physical machines running the crystallography beamlines to fully virtual between 2014 and 2018. 
Society & Non-profit organisations
1996-2020
Sees participation in society as a responsability and duty of all. Has always tried to contribute unselfishly to different projects.

Some examples
  • Active member in the Portuguese Free software association (2000, ANSOL)
  • Member of the executive board for the undergraduate students union (1996, AEFCT)
  • Member of the Pedagogic Council for FCT.UNL (1996-2000)
  • Member of the executive board of young researchers association (2004/2005, ABIC)
  • Chairman of the General Assembly for the portuguese younger researcheres association (2005/2006, ABIC)
  • Treasurer of the Society of Crystallographers in Australia and New Zeeland (SCANZ, 2014/2016)
  • Vice-President of the Society of Crystallographers in Australia and New Zeeland (SCANZ, 2017/2018)
  • President of the Society of Crystallographers in Australia and New Zeeland (SCANZ, 2019/2020)
  • Member of the winning bidding commitee to organize an IUCr in Australia.
Beamline / Instrument Scientist
2011-2020

In 2011 moved from a prestigious position as academic structural biologist (IEF-Marie Curie Fellow at Trinity Colleage Dublin) to a instrument scientist position in the Australian Synchrotron MX beamlines.


Here in less than 6 months converted himself into a indispensable troubleshooter of hardware and software issues with  attention to detail and heavy documentation writer of both of failures and of procedures being also strong assets. Taking very seriously quality control (QC) was always a major drive of his work. Heavily involvement on both software and design of the replacement of BLU-ICE with a microservice based beamline controls, hands on upgrade of optical elements (DCM for a microfocusing beamline),  sample changers (SAM robots), project managing a new goniometer install (involved in design, manufacturing, installing and acceptance testing),  detector upgrade (Eiger 16M) described in two publications. This position also allowed to improve on vital softskills like time management, team work, creative thinking and conflict resolution.  

Programming
2001-2020
Started by gained experience with Microsoft Visual Basic to interact with Microsoft Access database objects and create interactive applications to users. Later moved to administer LAMP servers where he learned to code dynamic database driven PHP-Mysql websites. During this period (2004-2008) was the webmaster of several sites running CMSs like Joomla and Wordpress as well as bulletin boards running Phpbb

In 2013 was introduced to python by Andy Bulka (website, linkedin) first on a one full day a week for 6 weeks basic python training. Two years later a second one day a week 6 weeks training on advanced python including object oriented programming. That training together with extentive hands on work at Australian Synchrotron MX beamlines but also with learnings from the genius coder Nathan Mudie changed his view of the world forever. Now felt no longer just a user but a driver on using software to control and manipulate hardware to collect better diffraction data as well as use software to improve on data analysis.

Non exhaustive list of projects involvement in coding
  • Attenuator wheel to control X-ray beam transmission at different energies (involved using Lambert–Beer law as well as control hardware via python and EPICS)
  • Migration of autoprocessing software to a Kubernetes based docker containers
  • Re-write of the python collection server logic to accomodate the migration from the old CCD based ADSC detectors to a Pixel array Eiger detector
  • Futher develop a python beamline library that kept abstraction at the application level from the beamline instrument where it ran
  • Involved on the design of the slow replacement of the monolith Blu-ICE to a microservices based ecosystem. 
  • Futher develop and maintain a QC based beamline setup GUI for delivering high quality beamline calibration to users. 
  • Implement diffraction rastering for sample centring at the Australian Synchrotron MX beamlines

I have produced these outcomes

Publications

List of peer-review publications

01

Protein Structures

Videos and pictures of protein structures

04

Thesis

Thesis document

02

Project Management

Project management experience

05

Invited Speaker

List of invited speaker talks

03

Others

Other content

06

My Skills

A complete team member

Versatile, creative, customer service oriented, self-driven, team builder, focused, organised and leader by example. 

01

Linux System Administration
95%
Network, Firewall, Secutiry
65%

Protein Crystallography
90%
Structural Biology
85%

Mail Server, Webserver, DNS
85%
Virtual Machines and Containers
75%

Hardware control with Python
80%
Data analysis using Python
75%

Soft skills

Managing people, Conflict management, Ability to persuade and inspire others, positive attitude in adversity and use of good humor to raise moral. 

02

25

years  in high
tech enviroments

10000

hours  collecting
at synchrotrons

500000

£ raised for
research projects

5

Countried that
lived and worked

My prior employers

Australian Nuclear Science and Technology Organisation

ANSTO
Research and Development

Australian Synchrotron

AS
Research and Development

University of Limerick

UL
Research and Education

Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa

FCT-UNL
Research and Education

Synchrotron Light Source Australia

SLSA
Research and Development

Trinity College Dublin

TCD
Research and Education

Instituto De Tecnologia Quimica e Biologica

ITQB
Research 

Fundacao para a Ciencia e Tecnologia

FCT
Research funding

My Blog

My Contact

Call Me

+44 1865 600 998

01

Contact Me

david@aragao.name

02

Visit Me

Oxfordshire, Uk

03

Contact Us
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