Ali Kaafarani

Unseen Bio

The Digital Gut, a visualization of a gut microbiome 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.

Memote

An example memote report for the E. Coli core model 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.

Data-Driven Design of Cell Factories and Communities

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

dnt.no

A digital map 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:

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: