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src/cv.md

@@ -0,0 +1,146 @@
+
+## Professional Experience
+
+2019 - Present: Software Engineer, Cisco, Ireland.
+
+2018 - 2019: Co-founder and CTO at ZEG.ai, London, UK.
+
+2017 - 2017: Cohort Member, Entrepreneur First, London, UK.
+
+2013 - 2013: Design Engineer, Powerak Ltd., Sunshine Coast, Australia.
+
+2009 - 2009: Intern Software Engineer, MCS Kenny, Ireland.
+
+2008 - 2008: Intern Software Engineer, Simulia (Dassault Systemes), Rhode Island, USA.
+
+## Academic Experience
+
+2014 - 2017: Postdoctoral Research Assistant, Mathematical Institute, University of Oxford.
+
+2013 - 2013: Research Associate, NUI Galway, Ireland.
+
+2009 - 2013: PhD Biomedical Engineering, NUI Galway, Ireland.
+
+2005 - 2009: BE Mechanical Engineering (1:1), NUI Galway, Ireland.
+
+## Fellowships and Awards
+
+* Digital Catapult Machine Intelligence Garage Cohort, Application Co-Author, 2019.
+
+* MSB Network Travel Grant, Co-Author, 2017.
+
+* MSB Network Travel Grant, Co-Author, 2016.
+
+* CRUK Oxford Kickstart Fund, Co-Author, 2015.
+
+* Associate Fellowship - 2020 Science Program, 2014-2016.
+
+* ICHEC Class B Project - Proposal co-author for time on Ireland’s national HPC cluster (500,000 CPU hours), 2011.
+
+* IRCSET PhD Fellowship under the EMBARK initiative (e72,000), 2009.
+
+* NUI Galway University Scholarship for academic performance, 2006 - 2008.
+
+* NUI Galway University Entrance Scholarship for academic performance, 2005.
+
+## Honours
+
+* Winner of Mathematical Sciences category, STEM for Britain awards for Early Career Researchers at the Houses of Parliament, 2017.
+
+* 2nd best paper in the established researcher category, RAMI bioengineering section conference, 2012.
+
+* RAMI bronze medal for best overall paper, RAMI bioengineering section conference, 2011.
+
+* Best paper, Sir Bernard Crossland Symposium, 2011.
+
+* Best presentation, NUI Galway CoEI research day, 2010 and 2011.
+
+* Shortlisted for the Young Investigator in Biomechanics award at the Endocardiovascular Biome- chanics Research (EBR) Congress, Marseille, France, May 2010.
+
+* Shortlisted for the Innovative Student Engineer Ireland award (Top 5) and Best Mechanical Engi- neering Graduate in the UK and Ireland (Top 3) at the SET awards 2009.
+
+* Best final year project, Engineers Ireland West division, 2009.
+
+* Frederic Barnes Waldron prize for top mechanical engineering graduate and MCS prize for best final year project in mechanical engineering, NUI Galway, 2009.
+
+## International Conference Presentations
+
+* J.A. Grogan, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, Modelling micro-vascular transport in
+tumours using intra-vital imaging data, Proceedings of the European Society for Mathematical and
+Theoretical Biology (ECMTB) Conference, Nottingham, United Kingdom, July 2016.
+
+* J.A. Grogan, B. Markelc, T.T. Tapmeier, R.J. Muschel, J.M. Pitt-Francis, P.K. Maini, H.M.
+Byrne, Parameter identification and validation of multi-scale vascular tumour models using imaging
+data, Proceedings of the IVth International Conference on Computational Bioengineering, Barcelona,
+Spain, September 2015.
+
+* J.A. Grogan, S.B. Leen, P.E. McHugh, Micro-scale modelling of metals for coronary stent ap-
+plications, Proceedings of the European Solid Mechanics Conference (ESMC), Graz, Austria, July
+2012.
+
+* J.A. Grogan, A. Bobel, S.B. Leen, P.E. McHugh, Bioreabsorbable stents: some recent develop-
+ments in analysis and design recommendations, Proceedings of the Endocardiovascular Biomechanics
+Research (EBR) Congress, Marseille, France, May 2012.
+
+* J.A. Grogan, B.J. OBrien, S.B. Leen, P.E. McHugh, A phenomenological corrosion model for
+biodegradable metals with application in bioabsorbable stent assessment and design, Proceedings
+of the International Workshop on Computational Mechanics of Materials (IWCMM), Limerick,
+Ireland, August 2011.
+
+* J.A. Grogan, S.B. Leen, P.E. McHugh, Modelling and experiments to aid performance assessment
+of biodegradable metallic stents, Proceedings of the Biomedical Engineering Society (BMES) Annual
+Meeting, Austin, Texas, USA, October 2010.
+
+* J.A. Grogan, S.B Leen, P.E. McHugh, A phenomenological model of corrosion in biodegradable
+metallic stents, Proceedings of the ASME Summer Bioengineering Conference (SBC), Florida, USA,
+June 2010.
+
+* J.A. Grogan, S.B Leen, P.E McHugh, Computational modelling of biodegradable metallic stents,
+Proceedings of the Endocardiovascular Biomechanics Research (EBR) Congress, Marseille, France,
+May 2010.
+
+## Invited Talks
+
+* Panellist at the Italy for Innovation series in the Italian Embassy, June 2019.
+
+* J.A. Grogan, A.J. Connor, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, A computational framework for multi-scale vascular tumour growth models, Computational Life Sciences Workshop, RWTH Aachen, Germany, June, 2016
+
+* J.A. Grogan, B. Markelc, R.J. Muschel, J.M. Pitt-Francis, P.K. Maini, H.M. Byrne, Assessing Mathematical Models of Oxygen Transport and Blood Flow in Tumour Micro-Vasculature Using Intravital Imaging Data, Proceedings of the Angiogenesis Gordon Research Conference, Rhode Is- land, USA, August 2015.
+
+## Symposium and Workshop Talks
+
+* J.A. Grogan, B. Markelc, I. Rodriguez-Villarreal, T. Alarcon, Pitt-Francis, P.K. Maini, H.M.
+Byrne, Integrating Multiphoton Imaging, Microfluidics Channels and Mathematical Modelling to
+Study Vascular Networks in Tumours, Cancer Research UK (CRUK) Oxford Annual Symposium,
+Oxford, United Kingdom, June, 2016
+
+* J.A. Grogan, B. Markelc, I. Rodriguez-Villarreal, T. Alarcon, Pitt-Francis, P.K. Maini, H.M.
+Byrne, Integrated Intravital Imaging and Mathematical Modelling of Vascular Networks in Tumours,
+Quantitative Biology in Oxford (QBIOX) Springboard Meeting, Oxford, UNited Kingdom, May 2016.
+
+## Teaching Activity
+
+* Inter-collegiate Course Tutor: Mathematical Physiology, University of Oxford.
+* Teaching Assistant: Finite Element Methods, National University of Ireland, Galway.
+* Lab Demonstration: Dynamical Systems, Doctoral Training Centre (DTC) - Systems Medicine and
+Mathematical and Computational Biology Modules, University of Oxford. Engineering Computing
+(Fortran) and Thermodynamics, National University of Ireland, Galway.
+
+## Peer Reviewing Activity
+
+* Annals of Biomedical Engineering
+* Acta Biomaterialia
+* Biomechanics and Modelling in Mechanobiology
+* BioMedical Engineering OnLine
+* Biomedical Materials Research: Part B
+* Bulletin of Mathematical Biology
+* Catheterization and Cardiovascular Interventions
+* International Journal of Mechanical Sciences
+* Journal of Biomedical and Health Informatics
+* Journal of Biomechanical Engineering
+* Journal of Theoretical Biology
+* Mathematical Biosciences
+* Materials Science and Engineering B
+* Nature Communications
+* PLOS Computational Biology
+* Scientific Reports - Nature

src/index.md

@@ -12,6 +12,6 @@ I enjoy writing software and live in the West of Ireland. My main interests are:
 
 This site includes a [technical](/blogs/technical) and [social](/blogs/social) blog, some info on previous and on-going [projects](/projects.html) and a [cv](/cv.html).
 
-My personal software projects are [self-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).
+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).
 
 I am on <a rel="me" href="https://mastodon.social/@compilz">Mastodon</a>, but not any other social media sites.

src/projects.md

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+Below is a summary of some of the commercial and academic projects I’ve worked on.
+
+## 2021
+
+### Porting the Webex App to Linux - Cisco
+
+<img border="0" alt="Webex on Linux" src="/static/WebexLinux.png" width="600">
+
+**Image:** The Webex App running on Ubuntu 22.04
+
+At [Cisco](https://www.cisco.com/) I was the technical lead on the project to bring the [Webex App to the Linux platform](https://help.webex.com/en-us/article/9vstcdb/Webex-App-for-Linux), supporting Ubuntu and Red Hat. My main technical work was on the installer, build system integration and platform integrations (e.g. keychain).
+
+#### Tools
+
+* `C++`
+* `CMake`
+* `Qt` UI Framework
+
+## 2019
+
+### 3D Modelling and Graphical Programming in the Browser - ZEG.ai
+
+<video width="350" height="250" controls>
+  <source src="/static/TableBuild_Speedup.mp4" type="video/mp4">
+Your browser does not support the video tag.
+</video>
+
+<video width="350" height="250" controls>
+  <source src="/static/TableMorph.webm" type="video/ogg">
+Your browser does not support the video tag.
+</video>
+
+**Videos:** Left - A browser-based 3D modelling tool based on graphical programming being used to create a 3D model of a table. Right - Scripted morphing of a table with photorealistic rendering.
+
+Most 3D model creation is highly manual with the typical process not being well suited for automation. While at [ZEG.ai](https://www.zeg.ai/) I worked on developing different ways to build 3D content that are better suited for automation. One project involved building a browser-based 3D modelling engine and a new graphical programming language. The engine was built using `C++` and integrated with `Three.js` and `Angular` in the browser using `WebAssembly`. The language was expressive and user-friendly, allowing commercial quality 3D models to be created by non-expert users. See the [ZEG.ai Sketchfab channel](https://sketchfab.com/zeg.ai) for nice examples.
+
+A related project involved creating a cloud-based renderer so that models built in the browser could be quickly used to create photo-realistic renders and animations. This involved Python wrapping the `C++` 3D engine with `PyBind` and integrating it with `Blender/Cycles` on `AWS`. Render tasks were managed with `RabbitMQ` and `Celery`.
+
+#### Tools
+* `C++`, `Python`, `PyBind`, `Clang`
+* `Angular`, `WebAssembly`
+* `ThreeJS`, `Blender`
+* `RabbitMQ`, `Celery`
+
+### Single Image Reconstruction of 3D Models with Deep Learning - ZEG.ai
+
+<video width="350" height="240" controls>
+  <source src="/static/MachineLearning.mp4" type="video/mp4">
+Your browser does not support the video tag.
+</video>
+
+**Video:** Fully automatic 3D model generation from a single image in the browser. This example was based on the `Pix2Mesh` architecture running on AWS.
+
+While at ZEG.ai I worked on several projects for automatic 3D model generation from single images. This involved researching, assessing and building on many state-of-the-art architectures from the academic literature. These covered 3D CNNs, custom octree-based architectures, graph CNNs and differentiable renderers. One particularly interesting approach was based on Neural Programming via RNNs allowing the graph created in the browser-based graphical programming language to be directly predicted. 
+
+#### Tools
+* `PyTorch`
+* `CNN`s, `RNN`s
+
+## 2018
+
+### Single Image Reconstruction of 3D Models with Computer Vision - ZEG.ai
+
+<video width="350" height="240" controls>
+  <source src="/static/ZegDemo.mp4" type="video/mp4">
+Your browser does not support the video tag.
+</video>
+
+**Video:** Automatic generation of 3D models from single images using computer vision and mesh morphing approaches.
+
+One of the early projects I worked on at ZEG.ai involved the generation of 3D models automatically from single images using computer vision techniques. The most effective approach involved item segmentation, classification and mesh morphing via optimization to best fit the resulting shape. This worked reasonably well for items with simple topology such as low poly containers, footwear, and clothing. I also evaluated more sophisticated computer vision approaches based on pose-estimation and non-rigid registration.
+
+#### Tools
+* `OpenCV`
+* `scikit-image`
+
+## 2017
+
+### Automatic 3D Model Generation - Entrepreneur First
+
+<img border="0" alt="Automatically generated lamps" src="/static/pjimage.jpg" width="350">
+<img border="0" alt="Automatically generated living room" src="/static/room.png" width="350">
+
+**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.
+
+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. 
+
+#### Tools
+* `Blender`
+* `Docker`
+
+### Microrheology - University of Oxford
+
+<img border="0" alt="Blood Flow" src="/static/CAD_RBC.png" width="600">
+
+**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).
+
+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.
+
+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.
+
+#### Relevant publications:
+
+* 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.
+
+### Semi-Flexible Polymer Networks - University of Oxford
+
+<img border="0" alt="Tracking" src="/static/cell_cell_communication.gif" width="600">
+
+**Image:** A simulation of two cells deforming a semi-flexible network (thanks to Dan Humphries).
+
+The extracellular matrix is a fibre network through which cells can communicate mechanically. The fibrous nature of the network allows cells to communicate over surprisingly large distances. Dr. Dan Humphries, Prof. Eamonn Gaffney and I investigated how the architecture of these fibre networks affects cell-cell communication.
+
+#### Relevant publications:
+
+* D.L. Humphries, **J.A. Grogan**, E.A. Gaffney, The Mechanics of Phantom Mikado Networks, Journal of Physics Communications, 2:055015, 2018.
+
+* 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.
+
+## 2016
+
+
+### Angiogenesis - University of Oxford
+
+<a href="https://jmsgrogan.github.io/MicrovesselChaste/">
+<img border="0" alt="Sprouting Angiogenesis" src="/static/corneal_angiogenesis.png" width="600">
+</a>
+
+**Image:** A simulation of sprouting angiogenesis in a corneal micropocket assay experiment.
+
+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.
+
+#### Relevant publications:
+
+* **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.
+
+* **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.
+
+
+### Radiotherapy  - University of Oxford
+
+<a href="https://jmsgrogan.github.io/MicrovesselChaste/">
+<img border="0" alt="Radiotherapy" src="/static/radiotherapy.png" width="600">
+</a>
+
+**Image:** A multi-scale, agent-based simulation of radiotherapy using a real tumour microvessel network.
+
+The responsiveness of tumours to radiotherapy depends on oxygen availability, which in turn depends on the structure of the tumour microvessel network. I studied the relationship between the 3D structure of the microvasculature and radiotherapy response. This involved simulating tumour growth and radiotherapy using multi-scale, agent-based soft tissue models.
+
+#### Relevant publications:
+
+* **J.A. Grogan**, B. Markelc, A.J. Connor, R.J. Muschel, J.M. Pitt-Francis, 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.
+
+## 2015
+
+### Stent Design - NUI Galway
+
+<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
+<img border="0" alt="Tracking" src="/static/images/tracking.png" width="600">
+</a>
+
+**Image:** Finite element simulation of stent delivery in a stenosed, curved, vessel.
+
+Accurate simulation of coronary stent deployment in the body can reduce reliance on costly experimental testing and accelerate device design. Detailed simulations, including curved, stenosed arteries and folded balloons encompass many challenging areas of solid mechanics. This includes, large deformations of anisotropic elastic materials, finite sliding contact, and construction of complex 3D geometries. I developed techniques for high-resolution stent deployment modelling, and applied them in studying bioabsorbable magnesium devices.
+
+#### Relevant publications:
+
+* **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.
+* **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.
+* **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.
+
+## 2014
+
+### Bioabsorbable Alloys - NUI Galway
+
+<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
+<img border="0" alt="Radiotherapy" src="/static/images/corrosion.png" width="600">
+</a>
+
+**Image:** 3D Scanning electron microscopy of a bioabsorbable magnesium alloy post corrosion.
+
+A new generation of temporary, bioabsorbable metallic medical devices is showing great promise. New computational techniques are required for simulating the bio-corrosion of these devices and predicting long term performance and risk. I developed several models of magnesium bio-corrosion, based on experimental testing of long-term corrosion of AZ31 alloy under static loading and applied these in the study of bioabsorbable metal stents.
+
+#### Relevant publications:
+
+* **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.
+* **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.
+* **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.
+
+### Metal Micromechanics
+
+<a href="https://github.com/jmsgrogan/PhDThesis_JGrogan/">
+<img border="0" alt="Tracking" src="/static/images/micromechanics2.png" width="600">
+</a>
+
+**Image:** A crystal plasticity finite element simulation of a deforming stent strut.
+
+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.
+
+#### Relevant publications:
+
+* **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, Influence of statistical size effects on the plastic deformation of coronary stents, Journal of Mechanical Behaviour of Biomedical Materials, 20:61-76, 2013.
+
+This is my personal site, all views are my own and do not represent those of current or previous employers.
+
+

src/publications.md

@@ -0,0 +1,51 @@
+
+## Journal Articles
+
+### 2019
+
+* 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.
+
+### 2018
+
+* 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.
+* 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.
+
+### 2016
+
+* 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.
+* 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.
+
+### 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.
+

src/software.md

@@ -0,0 +1,39 @@
+Title: Software
+
+I am a contributor to several open source projects, listed below. I have developed a number of preprocessing scripts and user subroutines for the Abaqus finite element solver, which are also below.
+
+## Microvessel Chaste
+
+A C++/Python library for spatial modelling of vascularized tissues:
+
+<a href="https://jmsgrogan.github.io/MicrovesselChaste/">
+<img border="0" alt="MicrovesselChaste" src="/static/MicrovesselChaste.png" width="600">
+</a>
+
+## PyChaste
+
+A Python wrapper for Chaste, a library for discrete modelling of soft tissues.
+
+<a href="https://jmsgrogan.github.io/PyChaste/">
+<img border="0" alt="PyChaste" src="/static/PyChaste.png" width="600">
+</a>
+
+## Chaste (contributor)
+
+A C++ library for computational physiology, including continuum and discrete soft tissue models.
+
+<a href="http://www.cs.ox.ac.uk/chaste/index.html">
+<img border="0" alt="PyChaste" src="/static/chaste.jpg" width="200">
+</a>
+
+## cppwg
+
+An automatic Python wrapper generator for C++ for PyBind or Boost Python, built on CAST-XML. [Link](https://github.com/jmsgrogan/cppwg).
+
+##  Stack3D
+
+A collection of scripts for segmentation of vessel networks from 3D image stacks. [Link](https://github.com/jmsgrogan/Stack3D).
+
+## Lamp Generator
+
+Scripts for algorithmically generating and rendering 3D models of lamps with Blender. [Link](https://github.com/jmsgrogan/gen-backend).

src/static/style.css

@@ -5,10 +5,9 @@ html{
 }
 
 body{
-    font-size: 14px;
     font-family: Verdana;
     color: #333333;
     padding: 20px;
-    max-width: 600px;
+    max-width: 800px;
     margin: 0 auto
 }