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Jamie J. Alnasir MPharm (Hons), PhD research candidate

I'm currently undertaking an PhD under the supervision of Dr. Shanahan at the Centre for Systems and Synthetic Biology. My research interests are in Computational Biology, Molecular Biology, Next Generation Sequencing, Bioinformatics and Cloud-computing.

I'm also interested in molecular visualisation for which I have developed Zeus, a molecular visualisation package and Neuropharmacology (I presented my Masters Thesis Characterisation of Cyclic Neuroprotective Binding Ligands with Prof. Austen at the Royal Society of Chemistry peptide symposium and St. Georges Research Day). {great quote on research from Philosopher Alan Watts}

My undergraduate study was in Pharmacy and Chemistry at Kingston University and St. Georges hospital medical school.  PharmCalc.com provides pharmacy and clinical calculations that run on the client using JavaScript and are conveniently accessed on a Smartphone). I have a commercial programming background in Delphi/C++/SQL in the  development of Client Server and nTier systems as well as database driven web development (PHP/MySQL).

A new project: Athena - Directed acyclic graphs to generate molecular visualisation

My Comprehensive home-page: http://www.al-nasir.com


News!

Software developments
New Software:
Android Molecular visualisation app (Zeus-Android alpha)
New Software: Android Clinical calculations app (PharmCalc-Android alpha)
New Live tool:
Web-based PDB structural analysis service

Conferences/Prizes
Conference: MatBio '16 conference, King College London, UK
I am to present a talk at the upcoming MatBio 16 conference, the title will be: Transcriptomics: Leveraging a MapReduce algorithm and Python for gene-expression analysis on Apache Spark. MattBio '16
Conference: CloudTech '16 IEEE conference, Marrakech, Morocco
I presented a workshop talk on using industry Bigdata tools in the field of Transcriptomics. The workshop focussed in detail on applying MapReduce to transcriptomics data (Drosophila Melanogaster was used) and discusses the Hercules distributed algorithm we have devised. Workshop talk abstract
CSPRC-16 (Computer Science Postgraduate Research Colloquium)
This year I served as Editor and coordinated this years Research Colloquium with fellow PhD student Diego Galeano. We have compiled a booklet of abstracts in which our work is also featured: CSPRC16-Abstract booklet, CSPRC16-programme.
Conference: ISCB 3D Sig (Structural Bioinformatics and Computational Biophysics)
Part of the ISCB (International Society for Computational Biology) event in Dublin, July 2015. I will present PDB-Hadoop (a Hadoop framework for parallelising legacy applications on the PDB)
Conference: Big Data Analytics Training Workshop, MSTI ENSIAS
Organised through the collaboration of the British Council, MSTI (Mediterranean Space of Technology and Innovation) Innovation and ENSIAS (École nationale supérieure d'informatique et d'analyse des systèmes), Rabat, Morocco.
CSPRC-15 (Computer Science Postgraduate Research Colloquium)
Conference: Developing data-driven biology within Morocco workshop
I will be presenting my research at the Developing data-driven biology within Morocco workshop which has been organised by The British Council and runs from 16th - 19th February.
Just announced as an RDA 5th Plenary Early Career Support Programme Winner:
RDA Fifth Plenary meeting in San Diego, March 9 to 11.

CSPRC-14 (Computer Science Postgraduate Research Colloquium)
Myself and another PhD student Ionut Tutu have coordinated this years Colloquium and have compiled a booklet of abstracts in which our work is also featured: CSPRC14-Abstract booklet, CSPRC14-programme.


Research

At Royal Holloway (PhD)
Transcriptomics on Spark Workshop – Introducing Hercules – an Apache Spark MapReduce algorithm for quantifying non-uniform gene expression

PDB-Hadoop: Parallelising Legacy applications on the Protein Databank using Apache Hadoop

Investigation into the annotation of protocol sequencing steps in the Sequence Read Archive

At St. Georges University of London Hospital Medical School (Masters)
Characterisation of cyclic neuroprotective PDZ binding ligands (abstract #10)
- also  presented as a Poster Presentation at RSC (The Royal Society of Chemistry) as part of the Protein and Peptide Science Group Early Stage Researcher Meeting in November 2011