Jamie J. Alnasir


  Dr. Jamie J. Alnasir M.Pharm (Hons), Ph.D. Researcher, IT Consultant, Photographer, amateur tennis player...


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Activities
2020  
November Imperial PFDC Workshop: Publishing Metrics
I attended an online Post-doctoral and Fellows Development Centre session on metrics as evidence of research impact.
 
I participated in the OligoArchive Review Meeting
This was between the EU Horizon 2020 team and Oligoarchive collaboration partners and I presented my contribution to the project. It involved Imperial College London and partners CNRS (Centre National de la Recherche Scientifique), Universitė Côte D'Azure, Eurecom and Helix-works.
 
FST Future Leaders Conference 2020: Science, Technology & Research in Universities
I attended the FST (Foundation for Science and Technology) Future Leaders Conference 2020 - Science, Technology & Research in Universities. The keynote presentation was by Professor Dame Nancy Rothwell, Vice-Chancellor, University of Manchester.
 
FST Future Leaders Conference 2020: Research and Innovation in Industry
I attended the FST (Foundation for Science and Technology) Future Leaders Conference 2020 - Research and Innovation in Industry. The keynote presentations were by Dr Loubna Bouarfa, Founder and CEO, Okra Technologies and Steve Rees, Vice-President for Discovery Biology, AstraZeneca.
 
FST Future Leaders Conference 2020: Science and Government
I attended the FST (Foundation for Science and Technology) Future Leaders Conference 2020 - Science and Government. The keynote presentation was by Professor Sir Patrick Vallance, Government Chief Scientific Advisor.
 
Imperial PFDC Workshop: Publishing Masterclass
I attended an online Post-doctoral and Fellows Development Centre session on publishing scientific papers in high-impact journals.
 
Imperial PFDC Workshop: Public Engagement
I attended an online Post-doctoral and Fellows Development Centre session on public engagement.
 
October Research paper released pre-print (aRxiv): Distributed Computing in a Pandemic: A Review of Technologies available for Tackling COVID-19
 
September I participated in the 1st Annual OligoArchive Meeting
This involved Imperial College London and partners CNRS (Centre National de la Recherche Scientifique), Universitė Côte D'Azure, Eurecom and Helix-works.
 
August Research paper released pre-print (BioRxiv): Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq
 
Imperial PFDC Workshop: Making the most of LinkedIn
I attended an online Post-doctoral and Fellows Development Centre session on LinkedIn.
 
July

June

May
Imperial: Consulting for Drug Development company


Ongoing consulting as part of my role at Imperial.
 
April Genomics Research with Genomics England - The 100,000 Genomes Project
I designed and implemented a distributed HPC (High-Performance Computing) genomics pipeline to search for viral insertions into human genomes. This work is in accordance with the Genomics England Clinical Interpretation Partnership (GeCIP), an international consortium of researchers, clinicians and trainees, established to improve understanding and practice of clinical genomics, and uncover new medical insights for patients.
 
March OligoArchive - DNA storage Research
Commenced work on the OligoArchive DNA-Storage Research project to overcome current storage technology limitations - i.e. durability and obsolescence - by devising and developing methods in which synthetic DNA is used as a storage medium. DNA, the biomolecule in which the genetic information of life is stored, is an extremely dense 3D storage medium with the theoretical capacity of 455 EB (Exabytes) per g, and can last millenia in a cold, dark environment. Current developments in DNA sequencing and synthesis, on which this technology is dependent, will ensure this is feasible in the not too distant future.
 
February New Research position at Imperial College London
Gained a Post-doctoral Research Associate position in Thomas Heinis's group (distributed software engineering and large-scale storage systems) in the Department of Computing.

Training: Completed two training courses from Nature Publishing's Master classes
I completed the following courses: i) Scientific writing and publishing - a three-part training course on research paper writing and publishing, also covering the writing and publishing of review papers ii) Focus on peer review.
 
January Workshop: Intro to Quantum Computing and circuits, ICR
I attended a taster session introducing quantum computing and the development of quantum-circuits using quantum gates applied to qubits.
 
2019  
December Secured Post-Doctoral Research Associate position at Imperial College, London for 2020
I will be pursuing research at Imperial College London from early 2020. More to follow.
 
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 (Ph.D.) [Computer Science]
Ph.D.: The Analysis of High-Throughput Biological Datasets Utilising Distributed Computing. I was awarded my Doctorate of Philosophy in Computer Science (Ph.D.) 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 a fellow Ph.D. 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 Ph.D. 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 M.Phil/Ph.D. Upgraded to Ph.D. 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.
 
  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 Ph.D. 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  
December Developed Athena molecular visualisation software for the Spark-64 (CPU) Solaris (OS) platform.
 
September Commenced Ph.D. programme, Royal Holloway University of London
 
2011-2012 Pharmacist Pre-registration training with GPhC [elected not to register as I gained a Ph.D scholarship]
   
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 Ph.D. 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.
 
2010  
October Developed Zeus molecular visualisation software to support my research masters project. Zeus was developed to view Brookhaven PDB files and was originally used to view interactions of PDZ binding ligands to the PDZ1 domain of PSD-95 protein, facilitating the labelling of residues which Rasmol, at the time, could not do. This allowed me to investigate putative ligands prior to synthesis. Zeus then was expanded to support other popular molecular file formats such as: Mol, Mol2/SYBYL, CSF, and XYZ formats. The ability to compute/infer hydrogen-bonds and hydrogen atoms (when not present in the model) was also added in the early release. The function to plot Ramachandran plots was added shortly after.
 
2009  
November Developed PharmCalc.com online Clinical and Pharmacokinetics calculations tool for educational purposes whilst studying clinical pharmacokinetics. The aim of PharmCalc is to harness modern client-side technology (JavaScript) to provide a time-saving means of performing common pharmacy calculations thereby assisting the pharmacist in the design and validation of dosage regimes that are efficacious and minimally toxic. The computational method allows for easy adjustment of calculation parameters, practically instantaneously, obviating the need to go through the tedious process of re-calculating by hand.
 

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