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Mojtaba Barzegari Profile picture
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Jun 17 • 10 tweets • 8 min read
(1/9)
I’m so glad to announce that the computational model I developed during my PhD is now a stand-alone software and has recently passed the strict review process of my favorite journal, Journal of #OpenSource Software 🤩

doi.org/10.21105/joss.…
Let me explain it a bit 👇
(2/9)
BioDeg is an #opensource cross-platform software written in #FreeFEM, C++, and Python for modeling the degradation of metallic #biomaterials and simulating the #biodegradation behavior of medical devices and #implants in #corrosion experiments.
(3/9)
The necessity and the details of the computational model of #biodegradable materials, which does the main simulation behind the scene, are already discussed in this Twitter thread, so make sure to have a look at it if you like to know more 🤓

(4/9)
Simulations in BioDeg can become complex and resource-demanding, so we used #HPC techniques to scale the computation to hundreds or thousands of CPU cores. This was done using the great toolkit #PETSc. More details are here 👇

(5/9)
BioDeg was originally developed to be used from #commandline, but then we added a #crossplatform easy-to-use #GUI to it, developed in #Qt, that can run on #Linux, #Windows, and #MacOS. The GUI allows the user to set up a simulation and monitor its progress 😎
(6/9)
BioDeg features a general #preprocessor as well, which facilitates producing appropriate mesh files for biodegradation simulations by embedding desired 3D shapes inside a container (acting as the medium/electrolyte) and adapting the mesh 🙃
(7/9)
Are you interested in trying it out? Then grab your own copy and see it in action. The source code as well as the pre-built binaries for Windows and Linux are available on #GitHub. We highly welcome your suggestions/comments/bug reports 😉

github.com/mbarzegary/Bio…
(8/9)
I should thank the editors and reviewers of @JOSS_TheOJ for their constructive comments. You can check out the open-review process of my submission here 👇
github.com/openjournals/j…
The review process of JOSS can make any software more standard, so HIGHLY RECOMMENDED 👍😇
(9/9)
Last but definitely not least, I appreciate the great support I received from my supervisor. Thank you so much @LiesbetGeris 🥰for providing me with the opportunity to target my favorite journal by converting my model into an #opensource software.
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More from @MojBarz

Mojtaba Barzegari Profile picture
Apr 1
(1/8)
I'm excited to share our latest code and paper
“A flexible and easy-to-use open-source tool for designing functionally graded 3D porous structures",
available now in Virtual and Physical Prototyping 🙂:

doi.org/10.1080/174527…

Read the story below 👇
(2/8)
Lattice infills are invaluable in many engineering applications. In the field of tissue engineering, Triply Periodic Minimal Surface (TPMS)-based lattices can be used to aid tissue growth by creating environments with adequate permeability and mechanical stimulus.
(3/8)
Do other tools exist to create TMPS infills? Yes, but are they also FOSS? Most not, and if they are they have limited functionality. This is why we created ASLI: A Simple Lattice Infiller. To also give users the flexibility to adapt the code to meet specific requirements🙂
Read 9 tweets
Mojtaba Barzegari Profile picture
Jan 31
(1/7)
One year has passed since I uploaded the first video to start my beloved personal project, #TuxRiders. And now, after one year, the project is where it should be. I love it more than before, and the feedback I receive now and then motivates me even more to keep it going.
(2/7)
I received many emails and comments during the past year on the topics discussed in the videos as well as suggestions to improve and expand the contents. I have always enjoyed replying to these emails to start a conversation, from which I learn new things a lot too.
(3/7)
I am very grateful to the people giving me their valuable feedback. It helps me improve the quality of the videos, make better plans for upcoming content, spread the message on the awesomeness of open-source philosophy, and make TuxRiders more useful for potential viewers.
Read 8 tweets
Mojtaba Barzegari Profile picture
Oct 13, 2021
(1/8)
Are you interested in reaction-diffusion systems? Also want to know more about coupling them with moving interface problems? Especially if it’s related to #HighPerformanceComputing and elaborated on it? Then, don't miss our recent publication😉👇
doi.org/10.1177/109434…
(2/8)
Reaction-diffusion systems coupled with moving interface problems (in which the boundary of the domain is part of the solution 🙂) have great importance in various real-world scenarios in chemistry and chemical engineering as well as environmental and life sciences.
(3/8)
As an example of such systems, we developed an #InSilico model of the #biomaterials degradation phenomena, in which the loss of material due to #corrosion (#biodegradation) leads to movement of the material-medium interface.
Read 9 tweets
Mojtaba Barzegari Profile picture
Jul 14, 2021
(1/8)
I'm glad to say that our latest paper in the Corrosion Science is now available online.🙂

"Computational modeling of degradation process of biodegradable magnesium biomaterials"
doi.org/10.1016/j.cors…
(2/8)
Biodegradable materials find important applications in designing supportive medical implants, but despite the advantages, assessing the uncontrolled degradation and release remain a challenge in practical use-cases.
(3/8)
Combining the insights obtained through several years of experimental research with computational (in silico) modeling approaches enables us to save lots of resources by studying the biodegradation of medical devices virtually prior to conducting any in vitro/vivo tests.💪
Read 9 tweets
Mojtaba Barzegari Profile picture
Jul 13, 2021
(1/6)
I'm very happy that we (finally) got an acceptance for our submitted paper in the Journal of Open Source Education, JOSE🙂.

"An open source crash course on parameter estimation of computational models using a Bayesian optimization approach"
doi.org/10.21105/jose.…
(2/6)
Parameter estimation is a crucial aspect of model development in science and engineering. In the proposed educational module, we have a look at the #Bayesian optimization processes in general and model calibration (parameter estimation) in particular.
(3/6)
For demonstration purposes, we implement a model parameter estimation process for a fitting problem step by step in Python such that the readers can adapt it to their own models and use-cases.

Codes are available in this repo: github.com/mbarzegary/edu…
Read 7 tweets

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