Hey there! I'm Ali!

I'm a software engineer and overall pretty cool nerd. Thank you for dropping by my little piece of the internet—I'm always excited to get visitors!

I currently work at Unseen Bio and live in Copenhagen together with my best friend and life partner Irene.

Perhaps you'd like to get to know me better, check out what I'm up to, or get in touch.

A picture of me, modified with Google DeepDream. The picture is dominated by teal, purple and blue colors and has psychedelic undertones. However, it has a smooth appearance and does not seem to produce any immediate pareidolia effect.

Stuff I'm into

Some of my life-long passions include snowboarding, splitboarding, kite surfing, cross-country skiing and mountain hiking. It's not all outdoors and adrenaline though; I try to make time to read books, and have accumulated a short list of favorites . Additionally, I've loved playing video games since I was 5 years old, and at this point, I don't think I will ever outgrow them.

I'm generally active in open source and have been part of GitHub's ubiquitous git hosting service since 2009. However, after Microsoft's acquisition in 2018, my feelings about the platform are lukewarm. GitLab is a serious contender in the DevOps platform space and currently my default choice for new projects. Sourcehut is also an appealing, minimalistic software development platform, and an interesting alternative to the bigger players. I'm also somewhat active on Stack Overflow, the definitive Q&A site for developers. Admittedly, I have more Qs than As, but hey, at some point we have enough Jon Skeets.

Did you know that there exists galaxies we can see, but never interact with because they're receding from us faster than light? No signal we send can ever reach them. If some of them harbor life, it is physically impossible for us to ever interact with those lifeforms. They're on their own, and so are we. Yeah, stop and consider that for a moment. Now let's solve FTL travel!

Unseen Bio

February 2020 to present
Copenhagen, Denmark
Role: Chief Information Officer

Unseen Bio is a fast-growing biotechnology startup which specializes in analyzing the gut microbiome, providing unique personalized insight into the health and composition of your gut.

We are 5 co-founders with a broad set of competences who came together to execute on a novel approach to gut microbiome analysis. By applying the technology from the DD-DeCaF project to the promising and rapidly advancing field of the gut microbiome, we found that we were in a position to generate a vastly improved and much more personalized picture of the microbiome, than what has been possible before.

To this aim, we built a unique interactive visualization of the microbiome and how it compares to a healthy reference gut. We then apply metabolic software to build a complete network model of each individual microbiome and the interactions between the different bacteria in that community. With this model, we can make useful predictions of how dietary changes will affect the microbiome positively or negatively.

The service is fully translated to Danish, German and English, and is available in Europe. Read more on unseenbio.com.

The Digital Gut, a visualization of a gut microbiome

Memote

Novo Nordisk Foundation Center for Biosustainability
May 2018 to February 2020
DTU, Lyngby Campus, Denmark
Role: Software Engineer

Memote (the metabolic model test suite) is a tool to analyze and score the quality of genome-scale metabolic models. It assists the process of model reconstruction by helping to quickly identify potential issues or best practice deviations from the community standard.

In close collaboration with the authors of Memote, I built an online service to help promote the tool and make it accessible to anyone with a browser. The service uses the official package and allows visitors to upload any metabolic model to be analyzed in our preconfigured online environment, and eventually receive a full report without having to install the application locally.

In the same period, I also made a handful of contributions to COBRApy, memote's underlying tool for constraint-based modeling.

Memote was published in Nature Biotechnology in 2020. A presentation of my modest career in academia is available on ORCID .

An example memote report for the E. Coli core model

Data-Driven Design of Cell Factories and Communities

Novo Nordisk Foundation Center for Biosustainability
December 2017 to February 2020
DTU, Lyngby Campus, Denmark
Role: Software Engineer

DTU Biosustain is an interdisciplinary research centre which develops new knowledge and technology to support the production of bio-chemicals using microbial production hosts called cell factories.

I was a senior developer and technical operations lead on Caffeine, a unique web platform which brings computer-aided design into the realm of metabolic engineering.

The project was funded through the EU Horizon 2020 programme, and I joined halfway into its 4 year duration. In the final phase of the project, we were invited to participate in the Business Acceleration Academy program of the BioInnovation Institute in Copenhagen, with the aim to develop a business plan and validate the future commercial potential of the product beyond its EU funding phase. This resulted in Metabolyzer, which has since joined forces with Unseen Bio.

As part of a 5 person team (a product owner, two bioinformaticians and two software engineers), I quickly received responsibility for large aspects of the project, including major architectural and technical decisions, collaboration and coordination with third party library communities, and fostering a culture of collecting data and metrics in order to make fact-based decisions.

The interactive map in Caffeine, showing parts of a pathway map with flux results for a metabolic model

Den Norske Turistforening (DNT)

Den Norske Turistforening (The Norwegian Trekking Association)
October 2011 to June 2017
Oslo, Norway
Role: Systems Developer

Den Norske Turistforening (DNT) is Norway's largest outdoor activity organisation with more than 300 000 members, which promotes trekking and mountain hiking, while preserving the Norwegian environment, nature and cultural values.

I was technical lead for the core web platform, Sherpa, which serves several functions:

  • The central web site (www.dnt.no), serving well over a million unique users yearly
  • Web sites for all 57 member associations, as well as cabin and campaign sites, amounting in more than 150 published sites
  • Integrated content management and administration tools
  • Membership services and integration with membership systems
  • Data management for DNTs core data (cabins, trails and guided tours)

Being hired explicitly to start the Sherpa project, I was involved in every part from the initial planning and development, to maintenance, operations and user support, in addition to general maintenance on older systems which the new platform eventually would replace. My responsibilities, varying somewhat over the course of the project, include:

  • Initial technology stack and architectural decisions
  • Development, configuration and deployment
  • Ensuring monitoring, error reporting, logging and system insights
  • Analyzing, prioritizing and handling automated error reports and user reported issues
  • Planning migration and data transition from older systems
  • User testing and quality assurance
  • Writing technical documentation, user guides and news bulletins
  • Technical support for users within the organization
A digital map

I am an experienced software developer and IT operations engineer with a pragmatic approach and preference for stability over experimentation. My motivation comes mainly from building something of value and use to others. Although I can still appreciate the intrinsic beauty in a well designed algorithm, elegant data structure or clever expression of computational logic, I see software systems as a means to an end; any perfectly engineered application does not matter if nobody uses it.

Having often worked in small teams with a large responsibility surface, I have out of necessity learned how to design low-maintenance systems. Instead of specializing in a narrow area, I learned how to be effective and productive across the stack. As a result, my standards for the development experience are very high: Short feedback cycles, stable, mature and battle-hardened software tools, well documented workflows and automation of mundane tasks. An application must be comprehensible and its behaviour transparent; to this end, automated testing, error reporting, logging, and metrics reporting are invaluable tools.

A crucial fact in software development: Code is much, much harder to read than it is to write. Therefore, documentation, readability and maintainability are extremely important to me. Not only for the code we write, but also for the libraries we depend on. I prefer to utilize established, mature tools that work and do not surprise the user, rather than experimenting with the latest fad of the week. This approach allows developers to get the job done and keep focus on higher levels of abstraction.

I am an avid Linux user who lives in the terminal. I invest a lot of time to learn the ins and outs of the tools I use regularly. For example, I use a tiling window manager and have learned most common operations in muscle memory, as well as the majority of the keybindings in my text editor. I find these skills essential in order to get things done effectively and leave mental capacity for higher level ideas.

I am patient and humble, and a reliable team player. I have a strong sense of fairness and value good reasoning over arguments from authority. Being an introvert and analytical by nature, I perform best on problems that are given due time for focus, deep work and reflection. An effective workplace needs to balance the need of close collaboration versus focused work, and I will not thrive in an environment which focuses solely on either extreme of that scale.

Core skills

My core technological skills revolve around Python and web programming. Here's a summary of the tools and technologies I'm skilled in and use regularly: