SeqTrainer: Encoding Synthetic Biology Data for Machine Learning
SeqTrainer is a software tool to facilitate the training of ML models on standardized data in SBOL stored in SynBioHub.
Sai Wong
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1 min readProfessional Summary
Hi, I’m Gonzalo Vidal a postdoctoral researcher at the Genetic Logic Lab, led by Chris Myers at the University of Colorado Boulder. I’m developing biological and computational tools to create platforms for engineering biological systems across scales. My aim is to design and deploy engineered organisms and ecosystems to produce food, medicine, shelter, and biotechnology for a happier, healthier, and sustainable humanity.
Education
PhD in Computer Science
Newcastle University
BS and Professional Title in Biochemistry
Pontifical Catholic University of Chile
BS in Natural and Exact Sciences
University of Chile
Interests
Synthetic Biology
Artificial Intelligence
Computational Biology
Software Engineering
Biocomputation
Automation
Genetic Networks
Genomic Networks
Complex Systems
Agriculture
Molecular Biology
Microbiology
Biochemistry
📚 My Research
My future research will be leading the DRAGGON Lab—Developing, Researching, and Architecting Genetic and GenOmic Networks—an interdisciplinary research laboratory committed to scientific and engineering excellence in synthetic biology, computational biology, and software development. We aim at creating platforms to engineer biological systems across scales using a computational-experimental integration in automated data-driven synthetic biology workflows.
Please reach out to collaborate 😃
Featured Publications
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OPA1 and disease-causing mutants perturb mitochondrial nucleoid distribution
In this work we studied the effect of OPA1 and different ADOA-causing mutants on nucleoid distribution. We used Opa1−/− MEF and overexpression of OPA1 mutants on WT MEF along with …
Josefa Macuada
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1 min read
LOICA: Integrating Models with Data for Genetic Network Design Automation
Logical Operators for Integrated Cell Algorithms (LOICA) is a tool for the design, modeling, and parametrization of synthetic genetic networks.
Novel Tunable Spatio-Temporal Patterns From a Simple Genetic Oscillator Circuit
In this study we uncover novel spatio-temporal patterns of gene expression generated by the repressilator in growing cell colonies, and establish a simple method for their design. …
Guillermo Yanez
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1 min readRecent & Upcoming Talks
Synthetic Biology Workshop
Workshop - Synthetic Biology - How to iterate a computer-aided DBTL workflow
Software for Synthetic Biology Workflows at SEED
Workshop - Software for Synthetic Biology Workflows - How to Improve Your Productivity and Impact
Research Interests
🏗️🧬 Synthetic Biology foundations and infrastructure
Architecting the foundations and infrastructure of synthetic biology, including standards, distributed databases, and modular software ecosystems for a computer-aided DBTL cycle, …
Trending
🤖🧑🏻🔬 Automated, modular, and scalable data-driven DBTL workflows
Developing automated, scalable workflows that leverage robotics, software, and cloud platforms to deliver programmatic DBTL pipelines for advanced biological engineering, …
🖥️🧠 AI/ML, mechanistic, and hybrid models for computer-aided biological engineering and research
Developing hybrid predictive models that combine mechanistic simulations with modern Artificial Intelligence (AI), including context-aware graph neural networks (GNNs) and agentic …
⚙️🦠 Biophysical and biochemical simulation engines
Developing biophysical and biochemical simulation engines to model the spatiotemporal interactions of microbial communities and their interactions with multicellular hosts, …
🧬🔧 Engineer genetic and genomic networks for intelligent biological systems
Use the developed infrastructure to design genetic networks for biocomputing using genetic logic circuits, in-vivo AI, and other unconventional computing such as phase-based …