Activities and CPD (Continual Professional Development)
In addition to my research activities, I am committed to CPD (Continuing Professional Development) and hence regularly undertake training that compliments my existing skillsets. Provided below is a non-exhaustive list of activities:
2024 |
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| October |
Passed UK CAA Private Pilot's Flight Crew License Check-ride
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I have completed my PPL training to gain my Private Pilot's Licence. The Skills Test check-ride flight involved:
- Pre-flight Planning & Departure (e.g Weather, Aircraft Performance, Mass and Balance)
- General Airwork (e.g. Stalls, Steep turns, Steep gliding turns)
- En-route Navigation (using paper chart, watch and dead-reckoning)
- Approach & Landing
- Emergency & Abnormal Procedures (e.g. Engine failures, Forced landing)
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| September |
The International Science Reserve (ISR):
I am now a member of the The International Science Reserve (ISR), an initiative of The New York Academy of Science. The institution mobilises the global scientific community to respond to complex, fast-moving situations, across borders, too big for any one country to handle – such as the next pandemic, a food systems catastrophe, or multiple climate-related weather disasters.
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| August |
Important updates for my professional apps: E6BJA (aka Jamie's Flight Computer) now has an advanced Carburettor Icing Risk Approximator for calculating the risk of carburettor icing in piston engines from ambient temperature and dewpoint. CliniCompute medical calculator app now has had its laboratory calculators section expanded to cover even more day-to-day laboratory calculations.
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| July |
Presented at UCL Research Computing Meeting – Condenser HPC Platform
I presented at the UCL Research Computing meeting to discuss the progress and status of the Condenser HPC platform, a cutting-edge research computing infrastructure developed by UCL’s Advanced Research Computing (ARC) team. The meeting was attended by key stakeholders, including senior professors and researchers from the social sciences faculties, as well as ARC leadership.
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Undertook training at RedHat — Ansible Automation Workshop
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Passed UK CAA Flight Radiotelephony Operator's Licence (FRTOL) practical exam
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| June |
UCL ECON Computational Research Seminar #June2024
I delivered a workshop for post-graduate researchers in the department of Economics at UCL. The workshop was based on my PLoS (Public Library of Science) educational paper "Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster" and introduced Standardisation of Pipelines using Workflow languages (in particular Nextflow) in economics computational research.
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| May |
I was invited by Google to Exploring AI and leadership: past, present and future (in partnership with the Aspen UK), at their offices in London.
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| April |
I peer reviewed a paper for: PLOS ONE (Public Library of Science).
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Added UCL Research Infrastructure Projects to the Portfolio section of this website.
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| March |
Invited to Google Developer Apps Community Insights (ACI), providing feedback (as an App Developer) on the following areas: Defining Excellence in Development, LLM Developer API and the The Importance of App Features
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| February |
CliniCompute Now Available on Apple App and Google Play Stores: A New Era for Medical Mobile App Software
Leveraging the foundation established by PharmCalc in 2009, a pioneering online tool for clinical and pharmacokinetic calculations, CliniCompute marks a significant advancement in medical mobile app software. Available now for both Apple iOS and Android platforms, CliniCompute is specifically designed to support and complement the needs of healthcare professionals. It provides a comprehensive suite of clinical calculators, scores, and unit conversions, all aimed at enhancing the clinician's ability to make quick, accurate assessments supplemented by the valuable educational content CliniCompute provides.
CliniCompute harnesses the latest in mobile computing technology to ensure unparalleled accessibility to these key calculators, which operate flawlessly offline without any requirement for user registration. This not only continues the tradition of offering time-saving computational methods but also broadens the application's scope to cover a more extensive range of medical and clinical areas. In doing so, CliniCompute solidifies its commitment to supporting healthcare professionals with a platform that is both informative and indispensable in their daily practice.
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2023 |
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| December |
www.JamiesAviation.com E6BJA (E-6B) Flight Computer Launched on the Microsoft Apps store
 
The E6BJA Flight Computer App has now been developed as an Microsoft App and is available on the Microsoft Apps store. It has been built for a number of architectures: x64, x86, ARM64, ARM and is available on Windows.
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Conference: Science and Technology Facilities Council (STFC) CIUK-2023 (Computer Insights UK)
I attended the STFC CIUK-2023 held in Manchester. Amongst the themes of the conference, was the focus on large-scale HPC infrastructure that is optimised for AI applications such as LLMs (Large-Language Models). My colleague from UCL's ARC (Advanced Research Computing) department, Dr. Owain Kenway, gave a talk on Bridging the Professional Services/Academic gap.
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Undertook refresher training — Separate courses on Agile Project Leadership, Project Management and Research Funding Management
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| November |
New Role at
UCL (University College London)
Commenced my new role at UCL, in the ISD (Information Services Division). I'll be working with ARC (Advanced Research Computing) to provide Research Infrastructure, Services and Research Applications for the School of Life and Medical Sciences (SLMS), Geography, the Laws, Arts and Humanities, and Social and Historical Sciences (SLASH) and the Institute of Education (IOE).
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I peer reviewed a paper for: Briefings in Bioinformatics.
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| September |
DNA Storage paper published at ACM (Association for Computing Machinery) Computing Surveys:
Survey of Information Encoding Techniques for DNA
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www.JamiesAviation.com AirWeatherNOTAM app Launched on the Google Play store
 
The AirWeatherNOTAM app now been developed as an Android App and is available on the Google Play store.
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Jamie's Flight Computer E6BJA (E6-B) gains more than 8,000 active users across both the Apple and Android platforms.
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| August |
Article: Aiming Higher - Building the World's Most Comprehensive Flight Computer App, E6BJA outlines the journey of creating this powerful aviation app, inspired by the classic "whiz-wheel" and modern electronic flight computers. E6BJA is packed with features for pilots and professionals, ensuring simpler and quicker operations, better reproducibility, and enhanced calculation accuracy. Development involved tackling the challenges of native coding for both Apple and Android, providing a consistent user experience across platforms.
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| July |
I peer reviewed a paper for: PLOS Computational Biology.
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| May |
Jamie's Flight Computer E6BJA (E6-B) — launched in August on the Google Play store — gains ~3,000 users
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Zeus-Android Molecular Viewer re-released on the Google Play Store
The original Zeus-Android Molecular Viewer, based on an Open-GLES version of the Zeus desktop codebase, was first released in Oct 2014. Incremental changes and developments in Android, over almost a decade, resulted in some UI menu features became unsupported. Recently re-developed, this new version of Zeus-Android resolves this and has been further optimised. Users can display Brookhaven PDB, MOL/MOL2 (SYBL) and CSF molecular model file formats. Raw PDB (Protein Data Bank) molecular models in PDB files can be automatically downloaded from the Protein Data Bank at RSCB.org (Research Collaboratory for Structural Bioinformatics PDB).
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| March |
The Portfolio section of this website is re-organised and gets a technical revamp.
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| February |
My paper with Prof. Hugh Shanahan on a metric for data quality in RNA-Seq transcriptomics datasets published in Journal of Computational Biology:
Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq
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Jamie's Flight Computer E6BJA (E6-B) — launched in January on the Apple App store — gains over 500 users in just a few weeks.
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Passed UK CAA Flight-Crew License Private Pilot theoretical exam
- PPL 030 Flight Planning and Performance (A) (PPL030A)
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| January |
1K+ downloads and ~1,000 active devices for Jamie's Flight Computer E6BJA (E6-B) app — launched in August on the Google Play store
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I peer reviewed a paper for: PLOS Computational Biology.
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2022 |
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| October |
Jamie's Flight Computer E6BJA (E6-B) — launched in August on the Google Play store — gains over 500 users
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| September |
Manuscript formally accepted at The Journal of Computational Biology (JCB)
Watch this space!
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New Role at NatureMetrics Ltd, London
NatureMetrics are a world-leading provider of biodiversity monitoring data, using environmental DNA (eDNA) surveys, metabarcoding and more.
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| August |
www.JamiesAviation.com E6BJA (E-6B) Flight Computer Launched on the Google Play store
The Flight Computer tool at www.JamiesAviation.com has now been developed as an Android App and is available on the Google Play store.
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| June |
My 2020 COVID-19 research (2020 preprint at ArXiv.org) formally published at ADCAIJ (Advances in Distributed Computing and Artificial Intelligence Journal):
Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19
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| May |
Intra-exon RNA-Seq quality manuscript under review at a Computational Biology Journal
Watch this space!
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| April |
Logged over 120 take-offs and landings
Over 120 take-offs and landings logged in aircraft class SEP (Single-engine piston):
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| March |
www.JamiesAviation.com Flight Computer updated
The Flight Computer tool at www.JamiesAviation.com has been updated to include even more calculators. The tool now features the following easy to use and accurate calculators for computing aeronautical and flight variables:
- Wind components (crosswind and tailwind)
- Wind Correction Angle (WCA)
- Fuel calculations (including specific gravity, consumption and endurance)
- Pressure and Density Altitude
- Cloud base
- Dew point and humidity
- TAS (True Air Speed) to IAS (Indicated Airspeed) and vice-versa
- Ground speed
- Bank angle
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| February |
JamiesAviation.com: Aviation Weather Retriever command-line utility now available!
I have released my Aviation Weather Retriever command-line utility on JamiesAviation.com. Written in Java, the tool retrieves US NOAA (National Oceanic and Atmospheric Administration) reports — it is designed for pilots who are IT savvy and have a terminal window handy. I have released this simple tool that I personally use before flights to obtain raw METARs (Metereological Terminal Aerodrome Reports) and TAFs (Terminal Aerodrome Forecast). Obtaining the raw reports, which are easily interpreted by pilots, is often quicker than using a mobile app as they can be easily deciphered and the command syntax is also very straighforward.
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2021 |
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| November |
Manuscript formally accepted at Advances in Distributed Computing and Artificial Intelligence Journal (ADCAIJ)
Watch this space!
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| October |
Passed UK CAA Flight-Crew License Private Pilot theoretical exam
- PPL 060 Air Navigation (A) (PPL060A)
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| September |
Passed UK CAA Flight-Crew License Private Pilot theoretical exam
- PPL 090 Communications (A) (PPL090A)
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Conference talk:
MatBio 2021, Foundations of Mathematics for Bioinformatics, King's college London
I presented a talk at the MatBio '21
conference covering work done at Imperial, with our collaborators, on the nascent area of DNA storage, that is the use of DNA as a storage medium. The title of the talk is: Encoding information into DNA
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Passed UK CAA Flight-Crew License Private Pilot exams
Passed all 6/6 of the UK Civil Aviation Authority (CAA) Part-FCL (Flight Crew Licence) exams I sat in a single sitting, at the first attempt. 3 exams remain, which I have not yet attempted.
- PPL 010 Air Law (A) (PPL010A)
- PPL 020 Aircraft General (A) (PPL020A)
- PPL 040 Human Performance (A) (PPL040A)
- PPL 050 Meteorology (A) (PPL050A)
- PPL 070 Operational Procedures (A) (PPL070A)
- PPL 081 Principles of Flight (A) (PPL081)
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| August |
HPC (High-Performance Computing) educational paper published at PLOS Computational Biology:
Fifteen Quick Tips for Success with HPC, i.e. Responsibly BASHing that Linux Cluster
Featured on the front page of the July 2021 edition of PLos Comp. Bio.
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| July |
Imperial: Consulting for Drug Development company |
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| June |
Manuscript formally accepted at PLOS Computational Biology
Watch this space!
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| May |
PFDC (Post-doctoral and Fellows Development Centre) training
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| April |
Imperial: Consulting for Drug Development company
OligoArchive Review Meeting
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| March |
Imperial PFDC: The PostDoc Entrepreneur
I attended a Post-doctoral and Fellows Development Centre training course on entrepreneurship.
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Genomics England: Large-scale genome analysis of viral insertions
I am currently running a large-scale genomic analysis using the pipeline I developed to disover viral insertions. This work is part of the Genomics England Clinical Interpretation Partnership (GeCIP) with Imperial College London.
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| February |
I peer reviewed a paper for: Briefings in Bioinformatics journal, Oxford University Press.
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Imperial PFDC: Intellectual Property
I attended a Post-doctoral and Fellows Development Centre training course on how intellectual property rights impact research.
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| January |
Imperial PFDC: Project Management
I attended a Post-doctoral and Fellows Development Centre training course on project management.
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HPC training paper released pre-print (arXiv):
Ten Simple Rules for Success with HPC, i.e. Responsibly BASHing that Linux Cluster
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Imperial PFDC Workshop: Personal Pitching
I attended a Post-doctoral and Fellows Development Centre session on selling and pitching research and expertise
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2020 |
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| December |
Genomics England recognises research published in my COVID-19 pre-print: Distributed Computing in a Pandemic: A Review of Technologies available for Tackling COVID-19
This work was featured in their list of notable research: Publications leveraging Genomics England data assets and Research Environment
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Imperial PFDC/CfAE Workshop: Writing Tools for Research Publication Success
I attended a workshop run by Imperial's CfAE (Centre for Academic English) which focused on writing for STEM research.
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| November |
Imperial PFDC Workshop: Publishing Metrics
I attended a Post-doctoral and Fellows Development Centre session on metrics as evidence of research impact.
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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.
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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.
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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.
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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.
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Imperial PFDC Workshop: Publishing Masterclass
I attended a Post-doctoral and Fellows Development Centre session on publishing scientific papers in high-impact journals.
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Imperial PFDC Workshop: Public Engagement
I attended a Post-doctoral and Fellows Development Centre session on public engagement.
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| October |
Research paper released pre-print (arXiv):
Distributed Computing in a Pandemic: A Review of Technologies available for Tackling COVID-19
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| 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.
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| 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
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Imperial PFDC Workshop: Making the most of LinkedIn
I attended a Post-doctoral and Fellows Development Centre session on LinkedIn.
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July
June
May |
Imperial: Consulting for Drug Development company
Ongoing consulting as part of my role at Imperial.
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| 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.
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| 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.
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| 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.
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| 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.
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2019 |
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| 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.
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| November |
I peer reviewed a paper for: Briefings in Bioinformatics journal, Oxford University Press.
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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.
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| 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.
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| 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.
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| July |
Conference talk:
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.
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| June |
Conference: ICR Internal Annual Conference
I attended the Institute of Cancer Research's Internal Annual Conference, held at Royal Holloway.
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| 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
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| April |
I peer reviewed a paper for: IT Professional journal, IEEE.
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I attended an LTA (Lawn Tennis Association) Tennis Focus Group at the The National Tennis Centre, Roehampton.
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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.
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| March |
Conference: ICR Internal Informatics Conference
I attended the Institute of Cancer Research's Internal Informatics Conference, Sutton.
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| February |
I peer reviewed a paper for: Briefings in Bioinformatics journal, Oxford University Press.
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2018 |
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| 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
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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.
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| November |
Research paper goes out to print in Briefings in Bioinformatics:
The application of Hadoop to Structural Biology
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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.
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| 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
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| August |
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.
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| July |
Research review paper released pre-print (BioRxiv):
The application of Hadoop in Structural Bioinformatics
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Doctoral Graduation: Royal Holloway
My Doctoral degree was conferred on me in the official Doctoral graduation ceremony at Royal Holloway, University of London:
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| June |
Conference: ICR Internal Annual Conference
I attended the Institute of Cancer Research's Internal Annual Conference, held at Royal Holloway.
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| 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).
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| 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
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| March |
New Role at the
Insitute of Cancer Research, London
Commenced work as a Scientific Programmer in the Scientific Computing department.
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2014 |
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| 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.
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| 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.
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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.
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2013 |
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| December |
Developed Athena molecular visualisation software for the Spark-64 (CPU) Solaris (OS) platform.
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| September |
Commenced Ph.D. programme, Royal Holloway University of London
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| May |
Awarded Diploma in Photography from the Institute of Photography
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2011-2012 |
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Pharmacist Pre-registration training with GPhC [elected not to register as I gained a Ph.D scholarship] |
2011 |
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| November |
Conference poster: 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.
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| October |
First Aider Training and Certiication, Portsmouth
I undertook First aider training for which I was certified.
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| 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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2010 |
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| 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.
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2009 |
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| 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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