About
Articles by Mark
Contributions
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How can you compare R&D roles in academia and industry?
Academic R&D is obviously aimed primarily at publishing papers, and at securing further funding, growing the research group etc. Industrial R&D is often more focused on developing a putative product, or improving the process to develop the same. The academic researcher therefore has greater flexibility in the domain of study, and this is more suitable for fundamental or exploratory research.
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What techniques can you use to evaluate deep learning models in drug discovery?
I applaud the suggestions that we must seek to apply 'data cleaning' to chemical structures before using these in ML/AI models. The desirable state is to have the correct structure in terms of basic structure, but also stereochemistry, tautomeric state, presence of isomers. I know full well , from my time managing large chemical structure collections that this ideal state is not always achieved. Sometime the only solution to resolving structural ambiguity is experimental data such as crystallography or NMR data. In many cases these are not available and we must accept ambiguity or 'noise' in structure data.
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What are the advantages and disadvantages of using Python with Linux containers and orchestration tools?
As mentioned previously Conda is a great tool for managing and resolving python dependency issues. Conda is great but Mamba is maybe even better. I have found it to be much faster, and also to often perform better in resolving complex dependency issues. Do try it. Python tooling continues to get better and better.
Activity
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🔍 Attention Academic Researchers! Are you ready to meet the evolving requirements of open-access journals without the headache? At Rancho…
🔍 Attention Academic Researchers! Are you ready to meet the evolving requirements of open-access journals without the headache? At Rancho…
Liked by Mark Forster
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Felix Bänsch (Beilstein-Institut, Frankfurt/Main) and I presented the latest progress in the development of InChI at the GCC conference in Bad Soden…
Felix Bänsch (Beilstein-Institut, Frankfurt/Main) and I presented the latest progress in the development of InChI at the GCC conference in Bad Soden…
Liked by Mark Forster
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TCR-Like (by some termed TCRm) antibodies represent a unique source of engineered antibodies extending the reach beyond their natural function by…
TCR-Like (by some termed TCRm) antibodies represent a unique source of engineered antibodies extending the reach beyond their natural function by…
Liked by Mark Forster
Experience & Education
Licenses & Certifications
Projects
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Advisory board Member for Bioexcel centre of excellence in computational biomolecular research.
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I was pleased to serve as a scientific / industry advisor to the Bioexcel project. This helped to establish a European centre for excellence in computational biomolecular research.
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Invited member of advisory panel for Nature scientific data
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I greatly enjoyed my time on the advisory panel related to the creation of the journal Nature "Scientific Data". This is one of a new generation of 'data journals' where appropriate credit and reference can be provided to the creators or guardians of innovative and important data sets.
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Lead organiser for Molecular Informatics Open Source Software (MIOSS) Conference
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Second conference of molecular informatics open source software (MIOSS).
At this conference I was presented with the Blue Obelisk for contributions to open source software. -
Chair of Elixir industry advisory committee
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It was an honour to chair the industry advisory committee for the Elixir infrastructure project. This involved cross company collaboration, networking and leadership aimed at securing the pan European open access data infrastructure.
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Chair of scientific advisory board for OpenPHACTS IMI project
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Coordinate and lead scientific assessment and feedback to technical and project staff on the
Open pharmacological spaces (OPS) semantic web data integration project. -
Accelerating Discovery by Mining and Visualising Integrated Chemogenomics Data
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This Syngenta and Rothamsted colaboration project, has a focus on extending the Ondex data integration toolkit by adding 'chemical intelligence' to the existing software toolkit. This will provide enhanced capabilities for chemical structure visualisation , and the ability to link together datasets of (for example) internal and external chemical structure repositories. External datasets will include public chemical bioactivity resources such as the ChEMBL resource hosted at EMBL-EBI. This will…
This Syngenta and Rothamsted colaboration project, has a focus on extending the Ondex data integration toolkit by adding 'chemical intelligence' to the existing software toolkit. This will provide enhanced capabilities for chemical structure visualisation , and the ability to link together datasets of (for example) internal and external chemical structure repositories. External datasets will include public chemical bioactivity resources such as the ChEMBL resource hosted at EMBL-EBI. This will enhance the interpretation of internal chemical structure information, providing links to public information on genes and proteins, allowing chemists and biologists greater insight into the mechanisms of bioactivity.
As the Ondex toolkit is available under an open source license, all enhancements will also be made freely available to the scientific community as open source. This is intended to drive the adoption and uptake of the new tools and capabilities and contribute to open innovation.Other creators -
Lead organiser for Systems, Pathways, Interactions, Networks Open Source Software (SPIN-OSS) conference
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As a follow up to the first MIOSS event in 2011, I organised an open source software conference for tools related to biological systems, pathways, interactions and networks.
Thanks to the EMBL-EBI industry program for support towards this event. -
Lead organiser for Molecular Informatics Open Source Software (MIOSS) Conference
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I conceived and organised the first molecular informatics open source software (MIOSS) conference in 2011. Thanks to the Wellcome Trust for support to make this innovative event a reality.
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Founding member of Oracle Life Science User Group (OLSUG)
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User group aimed at establishing excellence is using Oracle tools for life science data storage and applications.
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Member of steering committee for Elixir EU FP7 Project 2007-2011
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It was a privilege to work with EMBL-EBI senior leadership on establishing the Elixir pan European data infrastructure.
I was Chair of Elixir work package 10, covering plants, agriculture, small molecules and environment.
Co-chair of Elixir work package 3, on industry needs and participation.
More activity by Mark
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I will be at Pistoia this week. Rancho will have a big presence. Please reach out if you would like to schedule a one-on-one meeting. We will also…
I will be at Pistoia this week. Rancho will have a big presence. Please reach out if you would like to schedule a one-on-one meeting. We will also…
Liked by Mark Forster
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One of our 'Local Hero' companies Theolytics have absolutely nailed the message that we want to get to the children in the schools we engage with…
One of our 'Local Hero' companies Theolytics have absolutely nailed the message that we want to get to the children in the schools we engage with…
Liked by Mark Forster
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Yesterday marked my last day as a Postdoctoral Researcher, and what an incredible adventure it has been! Over the years, I have had the opportunity…
Yesterday marked my last day as a Postdoctoral Researcher, and what an incredible adventure it has been! Over the years, I have had the opportunity…
Liked by Mark Forster
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𝗪𝗲’𝘃𝗲 𝗱𝗲𝗰𝗶𝗱𝗲𝗱 𝘁𝗼 𝗼𝗳𝗳𝗲𝗿 𝗼𝘂𝗿 𝗽𝗹𝗮𝘁𝗳𝗼𝗿𝗺 𝗮𝘀 𝗼𝗽𝗲𝗻 𝘀𝗼𝘂𝗿𝗰𝗲 - 𝗵𝗲𝗿𝗲’𝘀 𝘄𝗵𝘆. We will no longer be selling our…
𝗪𝗲’𝘃𝗲 𝗱𝗲𝗰𝗶𝗱𝗲𝗱 𝘁𝗼 𝗼𝗳𝗳𝗲𝗿 𝗼𝘂𝗿 𝗽𝗹𝗮𝘁𝗳𝗼𝗿𝗺 𝗮𝘀 𝗼𝗽𝗲𝗻 𝘀𝗼𝘂𝗿𝗰𝗲 - 𝗵𝗲𝗿𝗲’𝘀 𝘄𝗵𝘆. We will no longer be selling our…
Liked by Mark Forster
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Hey everyone, this isn’t the easiest post to write, but with the biotech sector facing some challenges, my role was unfortunately impacted while I’ve…
Hey everyone, this isn’t the easiest post to write, but with the biotech sector facing some challenges, my role was unfortunately impacted while I’ve…
Liked by Mark Forster
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🌟 Spent my Saturday morning at Diamond Light Source open day - truly inspiring! The facility is a hub of innovation, showcasing the incredible…
🌟 Spent my Saturday morning at Diamond Light Source open day - truly inspiring! The facility is a hub of innovation, showcasing the incredible…
Liked by Mark Forster
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Fantastic news that Science Magazine has again ranked Syngenta in the top five of the world’s science employers, and number one in agriculture – for…
Fantastic news that Science Magazine has again ranked Syngenta in the top five of the world’s science employers, and number one in agriculture – for…
Liked by Mark Forster
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We are excited to collaborate with Sapient to accelerate the next generation of their Human Biology Database. This partnership will enhance the…
We are excited to collaborate with Sapient to accelerate the next generation of their Human Biology Database. This partnership will enhance the…
Liked by Mark Forster
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This new python toolkit should be of interest to anyone with a focus on macromolecular structure work.
This new python toolkit should be of interest to anyone with a focus on macromolecular structure work.
Shared by Mark Forster
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Happy Open Access Week 2024! Open Targets is proud to contribute to #OpenAccess and #OpenScience initiatives and help improve the success rates for…
Happy Open Access Week 2024! Open Targets is proud to contribute to #OpenAccess and #OpenScience initiatives and help improve the success rates for…
Liked by Mark Forster
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