Jamie J. Alnasir


  Dr. Jamie J. Alnasir M.Pharm (Hons), PhD researcher, IT Consultant, Photographer, amateur tennis player...


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Activities
2019  
November Attended conference: Big Data LDN (London) 2019
The event hosts commercial data and analytics experts, presenting tools to deliver effective data-driven strategies. Attending are 130 leading technology vendors and consultants, 150 expert speakers in 9 technical and business-led conference theatres, with real-world use-cases and panel debates.
 
October Delivered Python Programming Course, ICR Sutton
I delivered the Python Programming course (3 days of lectures) with a colleague. The course was designed specifically for researchers at the ICR (Institute of Cancer Research) and Royal Marsden hospital.
 
September Applied Deep-learning to medical image anonymisation
I implemented and delivered a project that applies a pre-trained convoluted neural network to anonymise medical DICOM images. These contain patient identifiable information that has been burned into the pixels in scans which needs removal to enable ethical use and sharing of the images for research. The project is fully automated and a containerised solution provides easy invocation of the functionality and integration.
 
July Conference: MatBio '19, Foundations of Mathematics for Bioinformatics, King's college London
I presented a talk at the MatBio '19 conference discussing work I've been doing at the ICR, the title was: Fostering Reproducibility, Standardisation, Fault-tolerance and Deployability in Computational Pipelines using Nextflow Workflow Language - Adoption and Training at the ICR.
 
June Conference: ICR Internal Annual Conference
I attended the Institute of Cancer Research's Internal Annual Conference, held at Royal Holloway.
 
May Research paper (with Prof. Brian Austen et al.) goes out to print in American Journals of Chemistry Vol. 3, No. 01, pp. 1-11: Cyclisation of Cell-Penetrating PDZ-Binding Peptides Directed to PSD95
 
April I attended an LTA (Lawn Tennis Association) Tennis Focus Group at the The National Tennis Centre, Roehampton.
 
Organised a two day Scientific Programming Workshop (Nextflow Workflow language) for ICR Researchers, Scientists, and Bioinformaticians.
This workshop equips participants with a grounding in developing standardised, reproducible, easy to maintain and deploy computational pipelines. The course was delivered by Paolo di Tommaso and Evan Flodden (Nextflow Developers) of SeqeraLabs.
 
March Conference: ICR Internal Informatics Conference
I attended the Institute of Cancer Research's Internal Informatics Conference, Sutton.
 
2018  
December Research paper goes out to print in IJFCS (International Journal of Foundations of Computer Science) Vol. 29, No. 08, pp. 1355-1372: Transcriptomics: Quantifying Non-Uniform Read Distribution Using MapReduce
 
Suggested/Attended distinguished guest lecture: Structural biology and drug discovery: Fighting the emergence of resistance in cancer and mycobacterial infections - A talk by Sir Prof. Tom Blundell, Cambridge, given to the dept. of Computer Science, Royal Holloway, London
I (through colleagues) invited Sir Prof. Tom Blundell to the department of Computer Science at Royal Holloway to give our Distinguished Guest lecture on structural biology.
 
November Research paper goes out to print in Briefings in Bioinformatics: The application of Hadoop to Structural Biology
 
Talk: Developing and Standardising Computational pipelines using a workflow language, ICR Sutton/Chelsea (Videolinked)
The audience was a panel of researchers who routinely use HPC (High Performance Computing) in fields such as Genomics, Bioinformatics, Computational Biology, Drug discovery and Image analysis. The topic was Developing and Standardising Computational pipelines using a workflow language.
 
October Delivered Python Programming Course, ICR Chelsea
I delivered the Python Programming course (3 days of lectures). The course was designed specifically for researchers at the ICR (Institute of Cancer Research) and Royal Marsden hospital
 
August Attended conference: MatBio '18, Foundations of Mathematics for Bioinformatics, King's college London
I previously presented a talk at this conference (MatBio '16). This year I attended without giving a talk.
 
July Research review paper released pre-print (BioRxiv): The application of Hadoop in Structural Bioinformatics
 
Doctoral Graduation: Royal Holloway
My Doctoral degree was conferred on me in the official Doctoral Graduation Ceremony at Royal Holloway, University of London:

Dr. Jamie Alnasir
 
June Conference: ICR Internal Annual Conference
I attended the Institute of Cancer Research's Internal Annual Conference, held at Royal Holloway.
 
May Awarded Doctorate (PhD) [Computer Science]
PhD: The Analysis of High-Throughput Biological Datasets Utilising Distributed Computing. I was awarded my Doctorate of Philosophy in Computer Science (PhD) from the University of London (Royal Holloway).
 
April Delivered Python Programming Course, ICR Sutton
I delivered the Python Programming course (3 days of lectures). The course was designed by Dr. Igor Kozin, for researchers at the ICR (Institute of Cancer Research) and Royal Marsden hospital
 
March New Role at the Insitute of Cancer Research, London
Commenced work as a Scientific Programmer in the Scientific Computing department.
 
2017  
September Research paper goes out to print in JIB: A Novel Method to Detect Bias in Short Read NGS Data
 
Attended conference: MatBio '17, Foundations of Mathematics for Bioinformatics, King's college London
I previously presented a talk at this conference (MatBio '16). This year I attended without giving a talk.
 
March Lecture: CS3110/CS5110 Bioinformatics module, Royal Holloway, London
I delivered the guest lecture to Computer Science students for their CS3110/CS5110 Bioinformatics module. The talk focussed on Next-Gen. Sequencing (NGS) and Transcriptomics and briefly discussed cluster computing and the cloud for analysis of RNA-seq data.
 
2016  
September Developed system: Push notifications for iOS, Android for Choose-survey project.
I implemented the push-notifications system for the Choose survey project, for the department of Economics at Royal Holloway. Read more about it: Choose-Survey project.
 
July Conference: MatBio '16, Foundations of Mathematics for Bioinformatics, King's college London
I presented a talk at the MatBio '16 conference, the title was Transcriptomics: Leveraging a MapReduce algorithm and Python for gene-expression analysis on Apache Spark:

 
May Conference: CSPRC-16 (Computer Science Postgraduate Research Colloquium)
This year I was editor and co-organiser with another PhD student.

Conference: CloudTech-16, Marrakech, Morocco
I gave a talk at CloudTech. [ View slides ]:

 
2015  
September Developed New system: Choose-Survey Survey-Monkey integrated platform.
I developed a system conceived by the Economics department. Choose Survey is a survey delivery and respondent tracking system integrated with SurveyMonkey and the University's IT user authentication system. Choose Survey delivers university developed surveys to the user (targeted at currently enrolled undergraduate students) via an Android app and Wordpress derived mobile friendly site. Read more about it: Choose-Survey project.
 
July 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)
 
May Research paper goes out to print in GigaScience: Investigation into the annotation of protocol sequencing steps in the sequence read archive
 
Conference: Big Data Analytics Training Workshop, MSTI ENSIAS
I delivered a PhD research talk. This event was organised through the collaboration of the British Council, MSTI (Mediterranean Space of Technology and Innovation) and ENSIAS (École nationale supérieure d'informatique et d'analyse des systèmes), Rabat, Morocco:

 
May MPhil/PhD Upgraded to PhD Proper

CSPRC-15 (Computer Science Postgraduate Research Colloquium)
 
February 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.
 
February 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.
 
2014  
July Attending the JSPS UK-Japan Meeting titled "From Duplexes to Quadruplexes 0x2013 Understanding DNA Structure and Function" conference held at the University of Reading, showcasing collaboration between the UK and Japan.
 
June Attended conference: Fisher Centre for Computational Biology meeting
A special joint event involving the RA Fisher Centre for Computational Biology and the Bloomsbury Research Institute which is a centre of excellence on infectious diseases resulting from a joint venture between the London School of Hygiene & Tropical Medicine and UCL. RA Fisher Centre meetings aim to bring together UCL and Crick Institute research groups active in Computational Biology research.
 
  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.
 
2013  
September Commenced PhD programme, Royal Holloway University of London
 
2011-2012  
  Pharmacist Pre-registration training with GPhC [did not register]
2011  
November Conference: Royal Society of Chemistry (RSC): Protein and Peptide Science Group Early Stage Researcher Meeting, London
I presented my masters project "Characterisation of cyclic neuroprotective PDZ binding ligands" alongside PhD research, under the supervision of Prof. Brian Austen.

 
July Awarded Masters in Pharmacy/Chemistry (M.Pharm)
Masters: Characterisation of Cyclic Neuroprotective PDZ binding ligands. I was awarded my Masters from Kingston University and St. Georges hospital medical school.
 

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