Computational biology · Research · Systems
Quintero-L, O.
I build systems to understand systems.
I am a biologist and bioinformatician working at the intersection of biology and computing: from genomic data to the tools that make it possible to interpret them.
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Four perspectives, one connected problem
Scientific work connects organisms, measurements, software, and decisions. These are not isolated disciplines.
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Biological systems
Genomics, bioinformatics, and systems biology as a starting point.
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Computational systems
Reproducible workflows, software, and infrastructure for data analysis.
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Intelligent systems
Models and agents as research questions, not assumed achievements.
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Physical systems
Instruments, sensors, and the environment where measurements begin.
What connects it all
A map of how I think
I am driven by understanding how the systems around me work. Life, computing, and everyday processes are mysteries I enjoy exploring. My background in biology meets programming and electronics in that search.
Read the ideas and their connections
One central question, different ways to explore. Lines are conceptual relationships, not technical dependencies or experimental results.
Personal question
Understanding systems
I am driven by understanding how the systems around me work. Life, computing, and everyday processes are mysteries I enjoy exploring. My background in biology meets programming and electronics in that search.
Perspective
Life and biology
My background in biology is a starting point for exploring life: from sequences and organisms to the relationships that make them work.
Perspective
Code and computing
Programming is another way to explore systems: transform data, test procedures, and build tools for asking biological questions.
Perspective
Electronics and measurement
I am interested in exploring electronics to understand how sensors, instruments, and controllers connect what happens in the physical world with data and code.
Perspective
Everyday systems
Curiosity does not stay in the lab. It is also about the processes around me each day: observing them and asking how they work is part of the same search.
Way to explore
Models and agents
Models let us represent parts of a system and examine its behaviour. Scientific agents open another question: how to plan, evaluate, and revise an analysis without losing its limits or traceability.
Way to explore
Metabolic networks
Systems biology connects genes, reactions, and fluxes. The metabolic reconstruction in my thesis is a concrete way to study those relationships at genome scale.
Way to explore
Reproducible workflows
Understanding an analysis also means being able to follow it again: versioned code, defined environments, and documented steps connecting data with results.
Way to explore
From phenomena to data
Measurement connects a phenomenon with a question we can study. The lab ideas explore how to record conditions and observations so they can be interpreted.
Tool
Vector editor
Try your cloning before the bench: REBASE or custom enzymes, real sticky ends, and the resulting plasmid in a linked map and FASTA.
Explore on the sitePerspective
Connected lab
Devices for culturing, monitoring, and instrumentation that report to a central Home Assistant system. Each project shows its real status: what is still an idea is drawn as a blueprint.
Explore on the siteDocumented research
Andean potato genome
A master's thesis on genome assembly and annotation of the Colombia variety of Andean potato and the reconstruction of a genome-scale metabolic model.
Explore on the siteDocumented research
RNA-seq pipeline
An undergraduate thesis on designing a reproducible pipeline to analyse RNA-Seq data from solid mutants of Andean potato.
Explore on the siteDocumented research
GenomeAgent
In development
A scientific agent that plans, runs, evaluates, and replans genome assemblies, with a language model that reasons and a harness that has the final say.
Explore on the siteLab project
Photobioreactor
Idea
A system for growing microalgae and cyanobacteria such as spirulina that measures light and drives the LEDs according to what the culture needs.
Explore on the siteLab project
Plant monitor
Idea
Substrate pH and moisture sensors that send an alert when the plants need water.
Explore on the siteLab project
DNA quantifier
Idea
Exploring how DNA quantifier measurements could reach the lab’s central system directly.
Explore on the siteLab project
Connected thermocycler
Idea
Exploring an IoT-connected thermocycler so that its records reach the lab’s central system.
Explore on the siteLab project
Flow hood
Idea
Exploring how to monitor the laminar flow hood from the lab’s central system.
Explore on the siteLab project
Shaking incubator
Idea
An incubator whose shaking is controlled by an ESP32 and integrated with Home Assistant to automate how it runs.
Explore on the site
Connects with
- Understanding systems ↔ Life and biology
Life is one of the systems I want to understand.
- Understanding systems ↔ Code and computing
Computing is another of the mysteries I enjoy exploring.
- Understanding systems ↔ Electronics and measurement
Exploring electronics brings me closer to how the physical world works.
- Understanding systems ↔ Everyday systems
The same curiosity starts with the processes around me every day.
- Life and biology ↔ Code and computing
Bioinformatics joins biological questions with computational methods.
- Code and computing ↔ Electronics and measurement
Code and controllers make it possible to read sensors and act on instruments.
- Electronics and measurement ↔ Everyday systems
Electronics is a way to explore everyday physical processes.
- Life and biology ↔ Metabolic networks
Metabolic networks describe relationships between reactions in an organism.
- Metabolic networks ↔ Models and agents
Metabolic reconstruction represents a system as a model of reactions and fluxes.
- Models and agents ↔ Code and computing
Computing lets us simulate models and run planning and evaluation loops.
- Code and computing ↔ Reproducible workflows
Computational procedures need steps and environments that can be repeated.
- Electronics and measurement ↔ From phenomena to data
Sensors and instruments turn physical observations into records.
- From phenomena to data ↔ Life and biology
Measurements let us study organisms and their conditions.
- From phenomena to data ↔ Reproducible workflows
Recording how data were obtained makes it possible to interpret and review an analysis.
- Andean potato genome ↔ Life and biology
My thesis addresses assembly and annotation of the Andean potato genome.
- Andean potato genome ↔ Metabolic networks
The thesis connects the annotated genome with reconstruction of a metabolic model.
- RNA-seq pipeline ↔ Life and biology
The undergraduate thesis studies RNA-seq data from Andean potato.
- RNA-seq pipeline ↔ Reproducible workflows
The pipeline organises the RNA-seq processing steps.
- RNA-seq pipeline ↔ Code and computing
The analysis turns repetitive procedures into a computational workflow.
- Vector editor ↔ Life and biology
The tool lets us explore cuts, ends, and sequence ligation.
- Vector editor ↔ Code and computing
Simulation and visualisation run in the browser.
- GenomeAgent ↔ Models and agents
GenomeAgent explores planning and evaluation of assembly strategies.
- GenomeAgent ↔ Reproducible workflows
The harness controls resources, validation, and analysis provenance.
- GenomeAgent ↔ Life and biology
The research question is how to assemble a genome under resource constraints.
- Connected lab ↔ Electronics and measurement
The projects explore connected instruments and controllers.
- Connected lab ↔ Everyday systems
The lab brings questions about physical processes into concrete projects.
- Connected lab ↔ From phenomena to data
Recording conditions and readings is a shared thread of the lab ideas.
- Photobioreactor ↔ Life and biology
The idea starts with culturing microalgae and cyanobacteria.
- Photobioreactor ↔ Electronics and measurement
It proposes measuring light and adjusting LEDs to the culture conditions.
- Plant monitor ↔ Life and biology
The idea seeks to observe plant substrate conditions.
- Plant monitor ↔ Everyday systems
Caring for plants connects an everyday question with sensors and alerts.
- Photobioreactor ↔ Connected lab
It is one of the documented lab ideas, with its published status.
- Plant monitor ↔ Connected lab
It is one of the documented lab ideas, with its published status.
- DNA quantifier ↔ Connected lab
It is one of the documented lab ideas, with its published status.
- Connected thermocycler ↔ Connected lab
It is one of the documented lab ideas, with its published status.
- Flow hood ↔ Connected lab
It is one of the documented lab ideas, with its published status.
- Shaking incubator ↔ Connected lab
It is one of the documented lab ideas, with its published status.
Lab
Lab network
Low-power devices transmit over LoRa to keep Wi-Fi uncongested; a LoRa gateway collects the readings and Home Assistant centralises and automates them.
Dotted blueprint: idea · pulsing outline: prototype · packets in transit: experimental or active
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Documented research
From a genome to a metabolic model
A thesis on genome assembly and metabolic reconstruction of the Colombia variety of Andean potato, available from the National University of Colombia repository.
Explore the research03 / 03
Background
Education and tools
The CV brings together my education and technical experience in a conventional format.
View CV