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jgrogan
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README.md
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README.md
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This repo has the content for https://www.jmsgrogan.com/
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## Building ##
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The site is built with my [dialann](https://git.jmsgrogan.com/jgrogan/dialann) generator.
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To set up the build environment do:
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``` shell
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git clone https://git.jmsgrogan.com/jgrogan/dialann
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cd dialann
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python -m venv .venv
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source .venv/bin/activate
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pip install .
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cd ..
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```
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To do the build:
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``` shell
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cd personal-site/src
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dialann --build_dir=../build
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```
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To deploy the build (assumes a particular server environment and local ssh setup):
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``` shell
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cd ..
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./infra/deploy.sh
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```
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## License ##
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Software and content in this repo are Copyright of James Grogan. You can use software under the GPLV3+, a copy of which can be found in the accompanying `LICENSE` file.
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Other content can be used under a CC BY-SA 4.0 license, see [here](https://creativecommons.org/licenses/by-sa/4.0/deed.en) for details.
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54
src/cv.md
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src/cv.md
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@ -1,7 +1,7 @@
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## Professional Experience
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2019 - Present: Software Engineer, Cisco, Ireland.
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2019 - 2022: Software Engineer, Cisco, Ireland.
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2018 - 2019: Co-founder and CTO at ZEG.ai, London, UK.
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@ -15,6 +15,8 @@
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## Academic Experience
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2023 - Present: Research Fellow, University of Galway, Ireland.
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2014 - 2017: Postdoctoral Research Assistant, Mathematical Institute, University of Oxford.
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2013 - 2013: Research Associate, NUI Galway, Ireland.
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@ -63,6 +65,56 @@
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* Frederic Barnes Waldron prize for top mechanical engineering graduate and MCS prize for best final year project in mechanical engineering, NUI Galway, 2009.
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## Journal Articles
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### 2019
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* M.O. Bernabeu, J Köry, J.A. Grogan, B. Markelc, A.B. Ricol, M. d’Avezac, J. Kaeppler, N. Daly, J. Hetherington, T. Krüger, P.K. Maini, J.M. Pitt-Francis, R.J. Muschel, T. Alarcón, H.M. Byrne, Abnormal Morphology Biases Haematocrit Distribution in Tumour Vasculature and Contributes to Heterogeneity in Tissue Oxygenation, In Submission, 2019.
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### 2018
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* J.A. Grogan, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, The Importance of Geometry in the Corneal Micropocket Angiogenesis Assay, PLoS Computational Biology 14(3):e1006049, 2018.
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* D.L. Humphries, J.A. Grogan, E.A. Gaffney, The Mechanics of Phantom Mikado Networks, Journal of Physics Communications, 2:055015, 2018.
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### 2017
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* D.L. Humphries, J.A. Grogan, E.A. Gaffney, Mechanical Cell–Cell Communication in Fibrous Networks: The Importance of Network Geometry, Bulletin of Mathematical Biology, 79:498-524, 2017.
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* J.A. Grogan, A.J. Connor, B. Markelc, R.J. Muschel, P.K. Maini, H.M. Byrne, J.M. Pitt-Francis, Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues, Biophysical Journal, 112(9):1767-1772, 2017.
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### 2016
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* J.A. Grogan, B. Markelc, A.J. Connor, R.J. Muschel, J.M. Pitt-Franices, P.K. Maini, H.M. Byrne, Predicting the influence of microvascular structure On tumour response to radiotherapy, IEEE Transactions on Biomedical Engineering, 64(3):504-511, 2016.
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* E.L. Boland, J.A. Grogan, C. Conway, P.E. McHugh, Computer Simulation of the mechanical behaviour of implanted biodegradable stents in a remodelling artery, JOM: The Journal of The Minerals, Metals and Materials Society (TMS), 68:1198–1203, 2016.
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### 2014
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* J.A. Grogan, S.B. Leen, P.E. McHugh, Computational micromechanics of bioabsorbable magnesium stents, Journal of Mechanical Behaviour of Biomedical Materials, 34:93-105, 2014.
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* J.A. Grogan, S.B. Leen, P.E. McHugh, A physical corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, In Press, DOI:10.1016/j.actbio.2013.12.059, 2014.
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### 2013
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* J.A. Grogan, D. Gastaldi, M. Castelletti, F. Migliavacca, G. Dubini, P.E. McHugh, A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments, Review of
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Scientific Instruments, 34:094301, 2013.
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* J.A. Grogan, S.B. Leen, P.E. McHugh, Optimizing the design of a bioabsorbable metal stent using computer simulation methods, Biomaterials, 34:8049-60, 2013.
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* E. Birmingham, J.A. Grogan, G.L. Niebur, L.M. McNamara, P.E. McHugh, Computational modelling of the mechanics of trabecular bone and marrow using fluid structure interaction techniques, Annals of Biomedical Engineering, 41:814-26, 2013.
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* J.A. Grogan, S.B. Leen, P.E. McHugh, Influence of statistical size effects on the plastic deformation of coronary stents, Journal of Mechanical Behaviour of Biomedical Materials, 20:61-76, 2013.
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### 2012
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* J.A. Grogan, S.B. Leen, and P.E. McHugh. Comparing coronary stent material performance on a common geometric platform through simulated benchtesting, Journal of Mechanical Behaviour of Biomedical Materials, 12:129-138, 2012.
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### 2011
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* J.A. Grogan, B.J. O'Brien, S.B. Leen, P.E. McHugh, A corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, 7:3523-33, 2011.
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### 2010
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* F. Harewood, J. Grogan, P. McHugh, A multiscale approach to failure assessment in deployment for cardiovascular stents, Journal of Multiscale Modelling, 2:1-22, 2010.
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## Conference Proceedings
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* P.E. McHugh, J.A. Grogan, C. Conway, E. Boland, Computational modeling for analysis and
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design of metallic biodegradable stents, Journal of Medical Devices: Presented at the Design of
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Medical Devices Conference, Minneapolis, USA, April 2015.
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* J.A. Grogan, P.K. Maini, J.M. Pitt-Francis, H.M. Byrne, Simulating tumour vasculature at multi-
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ple scales, Proceeedings of the 6th International Advanced Research Workshop on In Silico Oncology
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and Cancer Investigation, Athens, Greece, November 2014.
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## International Conference Presentations
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* J.A. Grogan, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, Modelling micro-vascular transport in
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@ -15,3 +15,8 @@ This site includes a [technical](/blogs/technical) and [social](/blogs/social) b
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My personal software projects are [hosted here](https://git.jmsgrogan.com/). Many of my work projects are open source, you can find some through my [work profile](https://git.ichec.ie/jgrogan).
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I am on <a rel="me" href="https://mastodon.social/@compilz">Mastodon</a>, but not any other social media sites.
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Unless otherwise specified all content on this site was created by me and can be re-used under the terms of the [CC BY-SA 4.0 license](https://creativecommons.org/licenses/by-sa/4.0/deed.en).
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I can be contacted at: <br/> <img src="/static/contact.png" width=220px>
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Below is a summary of some of the commercial and academic projects I’ve worked on.
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Below is a summary of some of the commercial and academic projects I've worked on.
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## 2024 ##
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### Marinerg E-Infrastructure - ICHEC ###
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The [Marinerg](https://www.marinerg-i.eu/) project aims to build a European distributed research infrastructure for offshore renewable energy. ICHEC are part of a work-package to build the e-infrastructure to support the project, including the design of web portals to support facility access and a data management system. The project is at an early stage, but some of the content is open-source and available [here](https://git.ichec.ie/marinerg-i).
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#### Tools ####
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* `Django`
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* `Angular`
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### ICHEC Common Tools - ICHEC ###
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Recently at ICHEC we've started building up a collection of documentation and software tools to help us standardize some of our workflows across projects. The documentation takes the form of a [handbook](https://ichec-handbook.readthedocs.io/en/latest/src/frontmatter.html) which has a public version. The software takes the form of a collection of open-source [Python packages](https://git.ichec.ie/performance/toolshed), including functionality for technical report generation, system monitoring, batch task processing on HPC systems and workflow management.
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#### Tools ####
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* `Python`
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* `Jupyter Book`
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* `Gitlab CICD`
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### Hierarchical Storage Management API - ICHEC ###
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As part of the [IO-SEA](https://iosea-project.eu) project for developing next generation exascale storage systems, ICHEC developed an API and implementation for interfacing a collection of diverse storage backends under a hierarchical storage management (HSM) paradigm.
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The developed software package [Hestia](https://git.ichec.ie/io-sea-internal/hestia) is a C++ application including Http and S3 client and server implementations and an interface to to CEA's [Phobos](https://git.ichec.ie/io-sea-internal/hestia) tape storage library.
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#### Tools ####
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* `C++/CMake`
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* `Curl`
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* `RPM Packaging`
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## 2021
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@ -83,7 +118,7 @@ One of the early projects I worked on at ZEG.ai involved the generation of 3D mo
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**Image:** Left - An early prototype of an automatic shape generator for lamps. This idea later evolved into a powerful approach for general 3D model generation, such as the room and contents on the Right.
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While at [Entrepreneur First](https://www.joinef.com/) most of my activities were related to company building and customer research, however my partner and I did build a snazzy automatic lamp model generator on a 4-day coding binge. This was written from scratch in `Python` with `Blender` and `Cycles` integration in a `Docker` container, while my partner built a `React`/`Node` web platform for it. I’m quite proud of this one as it was pulled together very quickly under pressure.
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While at [Entrepreneur First](https://www.joinef.com/) most of my activities were related to company building and customer research, however my partner and I did build a snazzy automatic lamp model generator on a 4-day coding binge. This was written from scratch in `Python` with `Blender` and `Cycles` integration in a `Docker` container, while my partner built a `React`/`Node` web platform for it. I'm quite proud of this one as it was pulled together very quickly under pressure. The source code is [available here](https://codeberg.org/jmsgrogan/render-generator-backend).
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#### Tools
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* `Blender`
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@ -95,13 +130,13 @@ While at [Entrepreneur First](https://www.joinef.com/) most of my activities wer
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**Image:** A segmented tumour microvessel network and a computer simulation of red blood cells flowing through it (thanks to Dr. Miguel Bernabeu, University of Edinburgh).
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The availability of oxygen in tumours affects malignancy and responsiveness to treatments such as radiotherapy. Tumour oxygenation depends on how red blood cells are distributed throughout the microvasculature. Suitable rules for modelling the distribution of red blood cells in the pathological vasculature of tumours have not yet been determined. I worked on studying how red blood cells distribute at branching points in the tumour, and ultimately making better predictions of oxygenation. This study was in collaboration with Prof. Ruth Muschel’s group at the University of Oxford, Dr. Miguel Bernabeu at the University of Edinburgh and Prof. Tomas Alarcon’s group at the CRM, Barcelona.
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The availability of oxygen in tumours affects malignancy and responsiveness to treatments such as radiotherapy. Tumour oxygenation depends on how red blood cells are distributed throughout the microvasculature. Suitable rules for modelling the distribution of red blood cells in the pathological vasculature of tumours have not yet been determined. I worked on studying how red blood cells distribute at branching points in the tumour, and ultimately making better predictions of oxygenation. This study was in collaboration with Prof. Ruth Muschel's group at the University of Oxford, Dr. Miguel Bernabeu at the University of Edinburgh and Prof. Tomas Alarcon's group at the CRM, Barcelona.
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My role here was segmentation of 3D image stacks from mulit-photon microscopy in mice, design of microfluidics chambers for flow experiments, particle tracking for measuring red blood cell flux and help in post-processing and 3D visualization of experimental and simulation results.
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#### Relevant publications:
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* M.O. Bernabeu, J Köry, **J.A. Grogan**, B. Markelc, A.B. Ricol, M. d’Avezac, J. Kaeppler, N. Daly, J. Hetherington, T. Krüger, P.K. Maini, J.M. Pitt-Francis, R.J. Muschel, T. Alarcón, H.M. Byrne, Abnormal Morphology Biases Haematocrit Distribution in Tumour Vasculature and Contributes to Heterogeneity in Tissue Oxygenation, In Submission, 2019.
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* M.O. Bernabeu, J Köry, **J.A. Grogan**, B. Markelc, A.B. Ricol, M. d'Avezac, J. Kaeppler, N. Daly, J. Hetherington, T. Krüger, P.K. Maini, J.M. Pitt-Francis, R.J. Muschel, T. Alarcón, H.M. Byrne, Abnormal Morphology Biases Haematocrit Distribution in Tumour Vasculature and Contributes to Heterogeneity in Tissue Oxygenation, In Submission, 2019.
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### Semi-Flexible Polymer Networks - University of Oxford
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@ -115,7 +150,7 @@ The extracellular matrix is a fibre network through which cells can communicate
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* D.L. Humphries, **J.A. Grogan**, E.A. Gaffney, The Mechanics of Phantom Mikado Networks, Journal of Physics Communications, 2:055015, 2018.
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* D.L. Humphries, **J.A. Grogan**, E.A. Gaffney, Mechanical Cell–Cell Communication in Fibrous Networks: The Importance of Network Geometry, Bulletin of Mathematical Biology, 79:498-524, 2017.
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* D.L. Humphries, **J.A. Grogan**, E.A. Gaffney, Mechanical Cell-Cell Communication in Fibrous Networks: The Importance of Network Geometry, Bulletin of Mathematical Biology, 79:498-524, 2017.
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## 2016
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@ -128,7 +163,7 @@ The extracellular matrix is a fibre network through which cells can communicate
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**Image:** A simulation of sprouting angiogenesis in a corneal micropocket assay experiment.
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Sprouting angiogenesis is a process in which new vasculature is formed. It is of central importance in the diagnosis and treatment of many cancers. It is a complex combination of biophysical processes, which are the focus of much on-going research. I worked on the development and application of open-source software for multi-scale modelling of this process and integration with intravital imaging data, in collaboration with Prof. Ruth Muschel’s group at the University of Oxford.
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Sprouting angiogenesis is a process in which new vasculature is formed. It is of central importance in the diagnosis and treatment of many cancers. It is a complex combination of biophysical processes, which are the focus of much on-going research. I worked on the development and application of open-source software for multi-scale modelling of this process and integration with intravital imaging data, in collaboration with Prof. Ruth Muschel's group at the University of Oxford.
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#### Relevant publications:
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@ -155,8 +190,8 @@ The responsiveness of tumours to radiotherapy depends on oxygen availability, wh
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### Stent Design - NUI Galway
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<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
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<img border="0" alt="Tracking" src="/static/images/tracking.png" width="600">
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<a href="https://git.jmsgrogan.com/jgrogan/phd-scripts">
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<img border="0" alt="Tracking" src="/static/tracking.png" width="600">
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</a>
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**Image:** Finite element simulation of stent delivery in a stenosed, curved, vessel.
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@ -173,8 +208,8 @@ Accurate simulation of coronary stent deployment in the body can reduce reliance
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### Bioabsorbable Alloys - NUI Galway
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<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
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<img border="0" alt="Radiotherapy" src="/static/images/corrosion.png" width="600">
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<a href="https://git.jmsgrogan.com/jgrogan/phd-scripts">
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<img border="0" alt="Radiotherapy" src="/static/corrosion.png" width="600">
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</a>
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**Image:** 3D Scanning electron microscopy of a bioabsorbable magnesium alloy post corrosion.
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@ -190,19 +225,17 @@ A new generation of temporary, bioabsorbable metallic medical devices is showing
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### Metal Micromechanics
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<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
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<img border="0" alt="Tracking" src="/static/images/micromechanics2.png" width="600">
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<a href="https://git.jmsgrogan.com/jgrogan/phd-scripts">
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<img border="0" alt="Tracking" src="/static/micromechanics2.png" width="600">
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</a>
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**Image:** A crystal plasticity finite element simulation of a deforming stent strut.
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The struts of coronary stents are less thick than a human hair. At this size-scale the assumptions of continuum plasticity theory begin to break-down, as metallic grains become comparable in dimension to the the strut. Explicitly modelling individual grains when simulating the deformation of stent struts allows ‘statistical size effects’, resulting in unexpectedly low failure strains, to be investigated. I studied the deformation of stent struts using crystal plasticity theory for a range of candidate stent materials, including magnesium.
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The struts of coronary stents are less thick than a human hair. At this size-scale the assumptions of continuum plasticity theory begin to break-down, as metallic grains become comparable in dimension to the the strut. Explicitly modelling individual grains when simulating the deformation of stent struts allows 'statistical size effects', resulting in unexpectedly low failure strains, to be investigated. I studied the deformation of stent struts using crystal plasticity theory for a range of candidate stent materials, including magnesium.
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#### Relevant publications:
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* **J.A. Grogan**, S.B. Leen, P.E. McHugh, Computational micromechanics of bioabsorbable magnesium stents, Journal of Mechanical Behaviour of Biomedical Materials, 34:93-105, 2014.
|
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* **J.A. Grogan**, S.B. Leen, P.E. McHugh, Influence of statistical size effects on the plastic deformation of coronary stents, Journal of Mechanical Behaviour of Biomedical Materials, 20:61-76, 2013.
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This is my personal site, all views are my own and do not represent those of current or previous employers.
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@ -1,51 +0,0 @@
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## Journal Articles
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### 2019
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* M.O. Bernabeu, J Köry, J.A. Grogan, B. Markelc, A.B. Ricol, M. d’Avezac, J. Kaeppler, N. Daly, J. Hetherington, T. Krüger, P.K. Maini, J.M. Pitt-Francis, R.J. Muschel, T. Alarcón, H.M. Byrne, Abnormal Morphology Biases Haematocrit Distribution in Tumour Vasculature and Contributes to Heterogeneity in Tissue Oxygenation, In Submission, 2019.
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|
||||
### 2018
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|
||||
* J.A. Grogan, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, The Importance of Geometry in the Corneal Micropocket Angiogenesis Assay, PLoS Computational Biology 14(3):e1006049, 2018.
|
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* D.L. Humphries, J.A. Grogan, E.A. Gaffney, The Mechanics of Phantom Mikado Networks, Journal of Physics Communications, 2:055015, 2018.
|
||||
|
||||
### 2017
|
||||
|
||||
* D.L. Humphries, J.A. Grogan, E.A. Gaffney, Mechanical Cell–Cell Communication in Fibrous Networks: The Importance of Network Geometry, Bulletin of Mathematical Biology, 79:498-524, 2017.
|
||||
* J.A. Grogan, A.J. Connor, B. Markelc, R.J. Muschel, P.K. Maini, H.M. Byrne, J.M. Pitt-Francis, Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues, Biophysical Journal, 112(9):1767-1772, 2017.
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### 2016
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* J.A. Grogan, B. Markelc, A.J. Connor, R.J. Muschel, J.M. Pitt-Franices, P.K. Maini, H.M. Byrne, Predicting the influence of microvascular structure On tumour response to radiotherapy, IEEE Transactions on Biomedical Engineering, 64(3):504-511, 2016.
|
||||
* E.L. Boland, J.A. Grogan, C. Conway, P.E. McHugh, Computer Simulation of the mechanical behaviour of implanted biodegradable stents in a remodelling artery, JOM: The Journal of The Minerals, Metals and Materials Society (TMS), 68:1198–1203, 2016.
|
||||
|
||||
|
||||
### 2014
|
||||
* J.A. Grogan, S.B. Leen, P.E. McHugh, Computational micromechanics of bioabsorbable magnesium stents, Journal of Mechanical Behaviour of Biomedical Materials, 34:93-105, 2014.
|
||||
* J.A. Grogan, S.B. Leen, P.E. McHugh, A physical corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, In Press, DOI:10.1016/j.actbio.2013.12.059, 2014.
|
||||
|
||||
### 2013
|
||||
* J.A. Grogan, D. Gastaldi, M. Castelletti, F. Migliavacca, G. Dubini, P.E. McHugh, A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments, Review of
|
||||
Scientific Instruments, 34:094301, 2013.
|
||||
* J.A. Grogan, S.B. Leen, P.E. McHugh, Optimizing the design of a bioabsorbable metal stent using computer simulation methods, Biomaterials, 34:8049-60, 2013.
|
||||
* E. Birmingham, J.A. Grogan, G.L. Niebur, L.M. McNamara, P.E. McHugh, Computational modelling of the mechanics of trabecular bone and marrow using fluid structure interaction techniques, Annals of Biomedical Engineering, 41:814-26, 2013.
|
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* J.A. Grogan, S.B. Leen, P.E. McHugh, Influence of statistical size effects on the plastic deformation of coronary stents, Journal of Mechanical Behaviour of Biomedical Materials, 20:61-76, 2013.
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### 2012
|
||||
* J.A. Grogan, S.B. Leen, and P.E. McHugh. Comparing coronary stent material performance on a common geometric platform through simulated benchtesting, Journal of Mechanical Behaviour of Biomedical Materials, 12:129-138, 2012.
|
||||
|
||||
### 2011
|
||||
* J.A. Grogan, B.J. O'Brien, S.B. Leen, P.E. McHugh, A corrosion model for bioabsorbable metallic stents, Acta Biomaterialia, 7:3523-33, 2011.
|
||||
|
||||
### 2010
|
||||
* F. Harewood, J. Grogan, P. McHugh, A multiscale approach to failure assessment in deployment for cardiovascular stents, Journal of Multiscale Modelling, 2:1-22, 2010.
|
||||
|
||||
## Conference Proceedings
|
||||
* P.E. McHugh, J.A. Grogan, C. Conway, E. Boland, Computational modeling for analysis and
|
||||
design of metallic biodegradable stents, Journal of Medical Devices: Presented at the Design of
|
||||
Medical Devices Conference, Minneapolis, USA, April 2015.
|
||||
* J.A. Grogan, P.K. Maini, J.M. Pitt-Francis, H.M. Byrne, Simulating tumour vasculature at multi-
|
||||
ple scales, Proceeedings of the 6th International Advanced Research Workshop on In Silico Oncology
|
||||
and Cancer Investigation, Athens, Greece, November 2014.
|
||||
|
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