Fuzue Tech · Research Software Engineering

Precision software
for science that
moves fast

Fuzue builds research-grade tooling for laboratories and ML teams. We track the literature and implement what works — from custom hardware interfaces and bioinformatics pipelines to production ML systems and platforms.

#5
Poland · Company research output
Nature Index
20+
Years engineering &
scientific consulting
15M
Researcher conflicts analyzed
Follow The Grant
3
Open source lab tools
in development

What we do

Three modes of engagement

Every project is direct — you work with the technical lead from day one.

01
Laboratory
Informatics
Custom analysis pipelines, hardware integration, flow cytometry and bioreactor interfaces, bioinformatics tooling — built to support publication-quality research.
Julia Python ChiBio Flow cytometry
02
ML & Data
Engineering
Time series modeling, NLP and speech systems, deep learning fine-tuning, data warehouse design and transformation. We implement recent techniques from the literature — not just off-the-shelf pipelines.
PyTorch Time series NLP / STT Fine-tuning dbt / SQL
03
Platform
Engineering
Long-term software products from mobile to infrastructure — full-stack web, iOS, Android, CI/CD pipelines, server orchestration. Sustained delivery on production systems.
React Android PHP Ansible Docker Python Svelte Java C C++

Open source

Lab tools, built in public

An ecosystem of open-source software for wet lab automation and bioinformatics — developed in active collaboration with the Pinheiro Group at Human Technopole.

Released
densitree
Density-normalized clustering with minimum spanning tree construction for high-dimensional data. A state-of-the-art SPADE implementation that outperforms FlowSOM and PhenoGraph on standard benchmarks — usable for cytometry, single-cell, and any point-cloud data with imbalanced density.
Python Clustering SPADE Cytometry scikit-learn
densitree.fuzue.tech → github.com/fuzue/densitree →
Released
KinBiont.jl
An ecosystem of numerical methods for microbial kinetics data analysis — from preprocessing to result interpretation. Covers growth curve fitting, model selection, segmentation, and comparative analysis across experimental conditions. Developed with the Pinheiro Group at Human Technopole.
Julia Microbial growth Kinetics Model fitting
github.com/pinheiroGroup/KinBiont.jl → github.com/fuzue/pykinbiont → E. coli knockout growth atlas →
In development
GUIbiont
A graphical interface for bacterial growth curve analysis — clustering, mathematical model fitting, and integration with the KinBiont.jl library. Designed to make quantitative microbial growth analysis accessible without leaving the lab's workflow.
Julia KinBiont.jl Growth curves Clustering
github.com/fuzue →
In development
AutoGate
Automated gating for flow cytometry data. Removes the manual, subjective step of population gating with a reproducible, algorithm-driven pipeline — built to integrate with research workflows and produce publication-ready results.
Python Flow cytometry Gating Reproducibility
github.com/fuzue →
In development
ChiBio UI
A new control interface for the chi.bio open bioreactor platform — finer experimental control, better data export, and a more capable operator experience than the original firmware allows.
ChiBio Bioreactor Hardware Firmware
github.com/fuzue →
+
More tools in progress
github.com/fuzue →

Research output

An active research program

Fuzue participates in peer-reviewed research — not as a vendor, but as a collaborator embedded in the science.

Track 01 — Wet lab & bioinformatics
Microbial growth
& lab automation
Published
Nature Communications — Kinbiont project, Pinheiro Group, Human Technopole, Milan. Software contributions to bacterial growth analysis and automated flow cytometry pipelines.Read the article →View Nature Index profile →
In progress
Two further publications expected in 2025 — ongoing collaboration with the Pinheiro Group at Human Technopole, Milan.
#5
Poland · Company research output
Nature Index ranking — placing Fuzue alongside institutions far larger in headcount and budget. A consequence of the depth of collaboration, not volume.
Track 02 — Scientific software methodology
Engineering practices
for science
In progress
Rigorous software development practices for scientific pipelines: project planning, test-driven development, CI/CD, and reproducibility for research teams. Bridging the gap between software engineering discipline and scientific coding.
Ongoing
The open-source tools (GUIbiont, AutoGate, ChiBio UI) are developed with the same rigor — documented, tested, and built to outlast the turnover of a research group.

Selected work

Recent engagements

Click any project to read more about the problem and approach.

Human Technopole · Pinheiro Group · Milan
Bacterial growth instrumentation & bioinformatics
ChiBio hardware integration · flow cytometry pipelines · Nature Communications
Laboratory

Working with the Pinheiro Group at Human Technopole in Milan, we customised ChiBio bioreactor hardware to provide finer experimental control beyond what the standard firmware allows. We then built the daily-use interfaces for plate reader data analysis and automated flow cytometry gating pipelines, integrated into the Kinbiont framework.

The software work contributed directly to a peer-reviewed publication in Nature Communications — listed under Fuzue Tech as the affiliated company. This is the basis of the #5 ranking among Polish companies in the Nature Index, and a rare distinction for a company in any field.

→ Read the article → View Nature Index profile → View example analysis
Digi Sapiens · B2B contract
ML engineering & edtech platform development
App dev team lead · Android · data warehouse · speech-to-text alignment
ML / Data

As app development team lead at Digi Sapiens, work spanned the full technical stack: Android application development, data warehouse architecture, and a particularly demanding speech-to-text alignment problem — matching spoken audio to text transcripts at word and phoneme level for educational use.

The alignment problem is NP-complete in its general form. The work involved surveying recent literature and developing a practical solution that performed well within the constraints of a production platform.

→ Discuss a similar project
Follow The Grant · Investigative data journalism
Civic data pipeline: research conflict-of-interest investigation
15M relationships analyzed · European Science Journalism Award 2021 · BuzzFeed News, Frankfurter Rundschau, Business Insider
Civic Tech

Built the data engineering pipeline behind an award-winning cross-border investigation into undisclosed conflicts of interest in academic research. The pipeline processed and cross-referenced 15 million potential researcher–industry relationships to identify systematic non-disclosure of pharmaceutical ties.

The investigation was published in BuzzFeed News, Frankfurter Rundschau, Business Insider, and CIVIO. The project received the European Science Journalism Award 2021 from the European Federation for Science Journalism.

→ Read the investigation
Aula Education · Germany
Long-term platform development & DevOps
Full-stack engineering on a production edtech platform used in German schools
Platform

Multi-year engagement on the Aula learning platform, deployed across schools in Germany. Work covered the full stack: PHP and React application development, MariaDB database management, Android and iOS mobile apps, GitHub Actions CI/CD workflows, and Ansible-based server provisioning and orchestration.

The engagement demonstrates sustained delivery capacity on a production European SaaS product — from feature development to infrastructure reliability, across multiple concurrent workstreams.

→ Discuss platform work

Who we are

Edgar Zanella Alvarenga
Photo coming
Edgar Zanella
Alvarenga
Founder

Fuzue is a technology company focused on research software engineering. Edgar founded the company after 20+ years of consulting across Europe and Brazil, and leads technical direction on every project. Depending on scope, we bring in specialists and collaborators — the team scales with the work.

Edgar has a background in physics and has worked with clients including Dell, Siemens, the Brazilian government, and leading European research institutions. He served as CTO of Open Knowledge Brazil and has built civic technology tools used at national scale.

Current focus is laboratory informatics, scientific software methodology, and an open-source wet lab tooling ecosystem in collaboration with Human Technopole, Milan.

Laboratory & bioinformaticsJulia, Python, ChiBio, flow cytometry
ML & data engineeringPyTorch, time series, NLP, STT, deep learning fine-tuning, dbt
Backend & databasesPHP, Python, MariaDB / MySQL, REST APIs, Docker
Frontend & mobileReact, TypeScript, Android (Java/Kotlin), iOS
InfrastructureLinux, Ansible, GitHub Actions CI/CD
LanguagesPortuguese, Italian, Spanish, German, Polish (learning)

Get in touch

Start a
conversation

Laboratory, ML, and research collaboration projects are prioritised. Describe your project and we'll respond within 48 hours.

Or write directly:

contact@fuzue.tech →