Markus Covert and Mycoplasma

Mike's Notes

This is part of why I rebuilt Pipi 6 from memory.

Resources

References

  • Fundamentals of Systems Biology

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Last Updated

11/05/2025

Markus Covert and Mycoplasma

By: Mike Peters
On a Sandy Beach: 10/03/2022

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

In 2014, I read an article in Scientific American by Markus Covert at Stanford about the successful computer cellular simulation of Mycoplasma. It was a fascinating article that made me think about Pipi and whether it could have been better built during 2005-2008.

When my wife and I left Christchurch in 2014 to start a new life, I became curious about modern cloud computing and read a great deal. Then, I realised that PIPI was a very early form of cloud computing, and many of its features were 10 years ahead of their time. What a waste!

By 2016, I was mad about missing the opportunity and decided to rebuild Pipi as a core platform from memory.

From 2017 to 2019, Pipi 6 was built by fusing the rebuilt core platform with Covert Lab's open-source cellular simulation software. This process was challenging and resulted in an unusual architecture. Every process was given a random probability, with many positive and negative feedback loops. It was like composing music. (In hindsight, synesthesia helped a lot.)

From Wikipedia

Markus W. Covert (born April 24, 1973) 

is a researcher and professor of bioengineering at Stanford University who led the simulation of the first organism in software.[1][2][3] Covert leads an interdisciplinary lab of approximately 10 graduate students and post-doctoral scholars.[4]



From Covert Lab

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In Defence of Science

Mike's Notes

I support the concerns expressed in this open letter to the NZ Listener.

"On July 24, 2021, in the context of a review of the secondary school curriculum National Certificate of Educational Achievement (NCEA), seven University of Auckland professors and emeriti professors (known informally as the Listener Seven) published a letter titled "In Defence of Science" in the current affairs magazine New Zealand Listener, which generated considerable controversy for claiming indigenous knowledge (or mātauranga Māori) "falls far short of what can be defined as science itself." " - Wikipedia

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References

  • Reference

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  • Home > Ajabbi Research > Library >
  • Home > Handbook > Science

Last Updated

28/03/2026

In Defence of Science

By: Prof Elizabeth Rata, et al.
New Zealand Listener: 31/07/2021

A recent report from a Government NCEA working group on proposed changes to the Māori school curriculum aims “to ensure parity for mātauranga Māori with the other bodies of knowledge credentialed by NCEA (particularly Western/Pakeha epistemologies)”. It includes the following description as part of a new course: “It promotes discussion and analysis of the ways in which science has been used to support the dominance of Eurocentric views (among which, its use as a rationale for colonisation of Māori and the suppression of Māori knowledge); and the notion that science is a Western European invention and itself evidence of European dominance over Māori and other indigenous peoples.”

This perpetuates disturbing misunderstandings of science emerging at all levels of education and in science funding. These encourage mistrust of science. Science is universal, not especially Western European. It has origins in ancient Egypt, Mesopotamia, ancient Greece and later India, with significant contributions in mathematics, astronomy and physics from mediaeval Islam, before developing in Europe and later the US, with a strong presence acoss Asia.

Science itself does not colonise. It has been used to aid colonisation, as have literature and art. However, science also provides immense good, as well as greatly enhanced understanding of the world. Science is helping us battle worldwide crises such as Covid, global warming, carbon pollution, biodiversity loss and environmental degradation. Such science is informed by the united efforts of many nations and cultures. We increasingly depend on science, perhaps for our very survival. The future of our world, and our species, cannot afford mistrust in science.

Indigenous knowledge is critical for the preservation and perpetuation of culture and local practices, and plays key roles in management and policy. However, in the discovery of empirical, universal truths, it falls far short of what we can define as science itself.

To accept it as the equivalent of science is to patronise and fail indigenous populations; better to ensure that everyone participates in the world’s scientific enterprises. Indigenous knowledge may indeed help advance scientific knowledge in some ways, but it is not science.

Kendall Clements
Professor, School of Biological Sciences, University of Auckland

Garth Cooper, FRSNZ
Professor, School of Biological Sciences, University of Auckland

Michael Corabllis, FRSNZ
Emeritus Professor, School of Psychology, University of Auckland

Douglas Elliffe
Professor, School of Psychology, University of Auckland

Robert Nola, FRSNZ
Emeritus Professor, School of Philosophy, University of Auckland

Elizabeth Rata
Professor, Critical Studies in Education, University of Auckland

John Werry
Emeritus Professor, Department of Psychological Medicine, University of Auckland

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Pipi 7 (2020)

Mike's Notes

A Brief History of Building Pipi 7.

Resources

  • Resource

References

  • Reference

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Last Updated

30/05/2025

Pipi 7 (2020)

By: Mike Peters
On a Sandy Beach: 01/03/2021

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

When Pipi 6 was finished, it was already overdue for replacement, given what I had learned from building it.

2020 Starting

The most significant change was the adoption of microservice architecture. Each microservice has a separate database, logic, workflow and web presentation layer. There were 300 microservices and lots of drawings inside 6-sided polygons.


I must have left a big trail of smoke from my Google searches, because Google started calling me every two months. Initially, I ignored them, but they wanted to host Pipi on Google Cloud Platform (GCP).

So, I optimised the internal architecture for cloud hosting on GCP using their platform tools.

A rules engine was built to handle logic. CQRS messaging that included persistent data storage.

The platform's self-documentation utilised ColdFusion.

Influences

2020 Finish

It looked good, and then it was ready for a complete rebuild (not even a refactor). However, the microservices architecture wouldn't scale because of the growing complexity caused by the Covert cell simulator-derived components. Docker wouldn't work, and it would now require a Virtual machine (VM).

Back to the drawing board.

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Curious Web Almanac Results

Mike's Notes

A useful resource.

Resources

References

  • Reference

Repository

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Last Updated

11/05/2025

Curious Web Almanac Results

By: Mike Peters
On a Sandy Beach: 06/02/2020

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

The Web Almanac 2019 is just out. It is an insightful survey of websites and the technology behind them. All backed up by robust statistics.

" Our mission is to combine the raw stats and trends of the HTTP Archive with the expertise of the web community. The Web Almanac is a comprehensive report on the state of the web, backed by real data and trusted web experts. It is comprised of 20 chapters spanning aspects of page content, user experience, publishing, and distribution." -  HTTP Archive

It makes for a fascinating read. I found the report on the use of JavaScript in web pages the most interesting, but it also covers the use of 20 other subjects, such as CSS, CMS, etc.

It is available in many languages and has an annual edition starting in 2019.

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Pipi 6 (2017-2019)

Mike's Notes

These are my notes from memory on building Pipi 6.

Resources

References

  • PIPI 4 Development Plan

Repository

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Last Updated

15/02/2026

Pipi 6 (2017-2019)

By: Mike Peters
On a Sandy Beach: 03/01/2020

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

In 2014, I read an article in Scientific American by Markus Covert from Stanford about the successful computer cellular simulation of Mycoplasma.

In 2015, I realised that Pipi had been a very early form of cloud computing, and I had been right about many things, and also wrong about others. 

When building Pipi 4, I had been regularly told by developers from NZ Crown Research Institutes.

"It's over-engineered"

I think they were just jealous. Pipi 4 was a better system than what they had.

In 2016, I decided to rebuild Pipi from memory and convert it into a Software as a Service (SaaS) platform that could host a broader range of applications, be more helpful to more people, and financially support itself. But first, I needed to catch up with how software development had changed.

Changes in Software Development

Strong support for ColdFusion had disappeared, replaced by AJAX; XML was replaced by JSON, and Cloud Computing was the new thing. Computers were getting cheaper and faster, physical software books were getting harder to find, JavaScript was everywhere, and the internet was much quicker.

2017 Start

I was in Invercargill, and there was no one to work with. The NZERN archive was long gone, but I did find some copies of the NZERN website on the Internet Archive. Pipi 4 was never documented due to funding constraints, so I carried the design around in my head. However, I found a copy of the PIPI 4 Development Plan and still had the original software reference books.

So, working from 1st principles, I reconstructed the database core of Pipi without the ecological restoration parts.

  • I added multi-tenancy and 20+ metadata columns to all tables.
  • The previous monolithic architecture was replaced by loosely connected modules.
  • I figured out how to turn all non-core modules into plugins.
  • I chose domain-driven design (DDD) as the methodology for organising future applications to run on this platform.
  • I quickly built populated apps in space, health, particle physics, agriculture, film, construction, laboratory experiments, and wetlands to prototype and test the system's design for hosting various domains.
  • I decided to continue using ColdFusion (CFML) for the coding.
  • I then reverse-engineered the Covert Lab Mycoplasma cellular simulator to understand how it worked.

Pipi 6 was built by fusing the rebuilt core platform with Covert Lab's open-source cellular simulation software. This was challenging and led to an unusual architecture and the use of Markov Chain Monte Carlo (MCMC), even though I didn't know it was called that at the time.

Every process was given a random probability. And many positive and negative feedback loops.

It was like composing music (In hindsight, synesthesia helped a lot).

Influences

The internet has changed everything. I could access the ideas and experiences of Martin Fowler, Gregor Hohpe, David C. Hay, Len Silverston, and many more. There were talks on YouTube as well. TDAN still existed, and a small group of well-organised CFML developers wrote a lot.

And there now was a thing called DevOps.

Thank you

I'd like to give special thanks to two people in Invercargill: Lesley Catterall for encouraging me right when I needed it, and Martin Catterall for being a great sounding board about integration. I was very lucky to meet those two.

2019 Finish

It was all going to work. It was rough and took 3 years to finish. By the end of 2019, it was time to refactor.

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What Is Web Hosting, Exactly? Everything You Wanted To Know

Mike's Notes

I'm learning something new every day.

Resources

References

  • Reference

Repository

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Last Updated

11/05/2025

What Is Web Hosting, Exactly? Everything You  Wanted To Know

By: Mike Peters
On a Sandy Beach: 23/10/2019

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

Richard Kershaw of WhoIsHostingThis.com contacted me today to suggest a great web article titled "What Is Web Hosting, Exactly? Everything You Wanted To Know."

It is a comprehensive introduction to the different types of web hosting that are available.

His website has a lot of handy resources. Everything from cookies to .htaccess to pattern generators.

Another helpful reference source.

I have recently shifted to working on the front end of a headless project and have taken a crash course in CSS 3.0 and HTML5.

A lot has changed in 10 years. In 2009, I only used XHTML and CSS 2.0 and did not use JavaScript.

I'm planning to learn along the way. Also, check out Web Accessibility requirements for screen readers, etc.

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Lessons from 300k+ Lines of Infrastructure Code

Mike's Notes

Brikman gives a sobering presentation about the reality of DevOps rather than the hype.

The good, the bad and the ugly.

This is a short extract. Follow the links to read and watch the full presentation.

Resources

References

  • Reference

Repository

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Last Updated

11/05/2025

Lessons from 300k+ Lines of Infrastructure Code

By: Yevgeniy Brikman
QCon: 23/05/2019

Yevgeniy Brikman is the co-founder of Gruntwork, a company that provides DevOps as a Service. He's also the author of two books published by O'Reilly Media: “Hello, Startup” and “Terraform: Up & Running”. Previously, he worked as a software engineer at LinkedIn, TripAdvisor, Cisco Systems, and Thomson Financial.

From QCon London, March 30 2019.

"Yevgeniy Brikman shares key lessons from the “Infrastructure Cookbook” they developed at Gruntwork while creating and maintaining a library of over 300,000 lines of infrastructure code used in production by hundreds of companies. Topics include how to design infrastructure APIs, automated tests for infrastructure code, patterns for reuse and composition, refactoring, namespacing, and more."

"Brikman: Thank you all for coming. This is a talk, as Jonas mentioned, of the ugly layer beneath your microservices, all the infrastructure under the hood that it's going to take to make them work and some of the lessons we learned. There's not a great term for this. I'm just going to use the word DevOps, although it's not super well-defined. And one of the things I want to share is a confession about DevOps to start the talk off.

Hey, there it is. There's a limited range on this thing. So here's the confession - the DevOps industry is very much in the stone ages, and I don't say that to be mean or to insult anybody. I just mean, literally, we are still new to this. We have only been doing DevOps, at least as a term, for a few years. Still figuring out how to do it. But what's scary about that is we're being asked to build things that are very modern. We're being asked to put together these amazing, cutting edge infrastructures, but I feel like the tooling we're using to do it looks something like that.

Now, you wouldn't know that if all you did was read blog posts, read the headlines, everything sounds really cutting edge. Half the talks here, half the blog posts out there, they're going to be about, oh my God, Kurbernetes, and Docker, and microservices, and service meshes, and all these unbelievable things that sound really cutting edge. But for me as a developer, on a day to day basis, it doesn't feel quite so cutting edge, right? That's not what my day-to-day experience feels like. My day-to-day experience with DevOps feels a little more like that. You're cooking pizza on an iron with a blow dryer. This is your hashtag for this talk, #thisisdevops. This is what it feels like...."

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Gremlin Announces Free Tier for Their Chaos Experimentation Platform

Mike's Notes

Roll this into DevOps.

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  • Reference

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Last Updated

11/05/2025

Gremlin Announces Free Tier for Their Chaos Experimentation Platform

By: Daniel Bryant
InfoQ: 22/05/2019

"The Gremlin team has announced "Gremlin Free", which provides the ability to run chaos engineering experiments on a free tier of their failure-as-a-service SaaS platform. The current version of the free tier allows the execution of shutdown and CPU attacks on a host or container, which can be controlled via a simple web-based user interface, API or CLI.

At the end of 2017 the Gremlin team announced the first release of their chaos experimentation SaaS product that supported the coordination of multiple attacks on hosts and the associated infrastructure. In 2018 application-level failure injection (ALFI) was also added, which supported running attacks on individual application services or functions. One of the primary attacks throughout the evolution of the product has been the shutdown of instances, which was partly inspired by the Netflix Chaos Monkey -- one of the first chaos engineering tools within the cloud computing domain.

The Gremlin team has argued that although the Chaos Monkey tool is useful, it does require time to learn how to safely operate. The original tool also only supported AWS (although additional tooling has emerged that offers similar instance shutdown abilities within Azure and Google Cloud Platform). With the launch of Gremlin Free, the Gremlin team is aiming to reduce these barriers to running chaos experiments, and facilitate teams in quickly seeing the value from doing so.

For engineers looking to explore the new free tier, Tammy Butow, principal SRE at Gremlin, has created a "Shutdown Experiment Pack" that is available on the Gremlin website. This provides a detailed walkthrough for running five chaos experiments that shutdown cloud infrastructure hosts and containers on AWS, Azure, and GCP (for which cloud vendor accounts are required) and also shut down containers running locally with Docker.

InfoQ recently sat down with Lorne Kligerman, director of product, and discussed the motivations and future plans with Gremlin Free."

And you can read the rest of the interview here.

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Welcome to Learn Performance

Mike's Notes

Notes on web page load performance.

Resources

References

  • Reference

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Last Updated

11/05/2025

Welcome to Learn Performance

By: Mike Peters
On a Sandy Beach: 21/05/2019

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

I found valuable articles from the Google Chrome Team called "web.dev".

https://web.dev

The web performance section is about the loading speed of web pages and how to optimise it.

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Otherworldly Java: Gateway to the Moon and beyond

Mike's Notes

A recent talk at QCon London by Diane Craig Davis intrigued me. 
The talk is well worth watching.
  • JavaFX improves on Java Swing by requiring much less code to get things done.
  • Canvas enables on-the-fly rendering of millions of points for real-time animation.
  • Sean Phillips now works at John Hopkins.
  • NetBeans IDE looks great (not too cluttered).
  • I have only used Eclipse and Visual Studio to work with Java. Now I will switch to NetBeans.
  • Use Eclipse for XML technology.

Resources

  • https://www.infoq.com/presentations/java-science-aerospace
  • https://en.wikipedia.org/wiki/JavaFX
  • https://en.wikipedia.org/wiki/Three-body_problem
  • https://en.wikipedia.org/wiki/Apsis
  • https://en.wikipedia.org/wiki/Poincar%C3%A9_map
  • http://www.fxyz3d.org/

References

  • Reference

Repository

  • Home > Ajabbi Research > Library >
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Last Updated

18/04/2025

Otherworldly Java: Gateway to the Moon and beyond

By: Diane Craig Davis
QCon: 19/04/2019

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

A recent talk at QCon London by Diane Craig Davis intrigued me.

The talk is well worth watching.

"Diane Craig Davis is an astrodynamicist and principal systems engineer with NASA and USAF aerospace industry leader AI solutions. She designs spacecraft orbits with the Gateway trajectory team at Johnson Space Center in Houston, TX, and previously navigated spacecraft to Mars and comets at the Jet Propulsion Laboratory. She is the lead researcher for the Deep Space Trajectory Explorer." (from QCon)

The talk was about Deep Space Trajectory Explorer, a JavaFX-based trajectory design and visualization software package that features a mix of custom 2D and 3D visualizations.

Astrodynamicist Diane Craig Davis worked with JavaFX developer Sean Phillips to find a way to visualise the possible space trajectories of three body systems: the Earth, the Moon, and a spacecraft.

3 body systems are inherently chaotic.

The closest approach in an orbit is called a periapsis point. A collection of potential periapsis points is called a Poincaré map. Deep Space Trajectory Explorer enables a scientist to quickly and simply see a million possible orbits using a Poincaré map, and then whittle them down to find the best path for a trajectory.

Here are another 2 videos by Diane Craig Davis and Sean Phillips found on YouTube.


Sean Phillips also gave a great two-hour talk and demo on Javafx and Netbeans IDE at Java User Group Dahlgren.

Sean also created JavaFX 3D Library available on GitHub

"My new 3D library for JavaFX 8. F(X)yz provides useful primitives and more complex data visualization components that are unavailable in the base JavaFX 3D package."

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