https://github.com/multiomics-analytics-group/course_synthetic_biology_data
Slides for lecture "Leveraging existing biological data and making sense of it" part of DTU's Summer School on Synthetic Biology for Cell Factories
https://github.com/multiomics-analytics-group/course_synthetic_biology_data
course education slides
Last synced: 4 months ago
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Slides for lecture "Leveraging existing biological data and making sense of it" part of DTU's Summer School on Synthetic Biology for Cell Factories
- Host: GitHub
- URL: https://github.com/multiomics-analytics-group/course_synthetic_biology_data
- Owner: Multiomics-Analytics-Group
- License: apache-2.0
- Created: 2023-06-18T08:17:11.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-06-17T06:45:00.000Z (12 months ago)
- Last Synced: 2025-09-02T13:05:30.072Z (10 months ago)
- Topics: course, education, slides
- Homepage:
- Size: 45 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Synthetic Biology Data
Leveraging Existing Biological Data and Making Sense of it
## Abstract
## Objectives
- Show
- The value of **Open** and **standardised data**
- How to **generate** and **find** these data
- How to **access** and **use** them
- Some **examples**
## Content
- Introduction
- No data, no fun
- Objectives / material
- Open science
- FAIR data
- Ontologies
- Data sources - databases
- Working with these databases - GUI/API
- Sharing data
- Graphs/Networks
- Knowledge Graphs
- Use case
- Tools
- GraphML
- QA
## References
- [A parasite's perspective on data sharing](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258825/) YoSon Park; Casey S Greene *Gigascience*
- [Network biology: understanding the cell's functional organization](https://www.nature.com/articles/nrg1272) Albert-László Barabási; Zoltán N. Oltvai *Nat. Reviews Genetics*
- [Data-Driven Synthetic Cell Factories Development for Industrial Biomanufacturing](https://spj.science.org/doi/10.34133/2022/9898461) Zhenkun Shi; Pi Liu; Xiaoping Liao; Zhitao Mao; Jianqi Zhang; Qinhong Wang; Jibin Sun; Hongwu Ma; Yanhe Ma *BioDesign Research*
- [Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories](https://pubs.acs.org/doi/10.1021/acssynbio.7b00423) João G. R. Cardoso; Kristian Jensen; Christian Lieven; Anne Sofie Lærke Hansen; Svetlana Galkina; Moritz Beber; Emre Özdemir; Markus J. Herrgård; Henning Redestig; Nikolaus Sonnenschein *ACS Synthetic Biology*
- [Automating the design-build-test-learn cycle towards next-generation bacterial cell factories](https://www.sciencedirect.com/science/article/pii/S187167842300002X) Nicolás Gurdo; Daniel C. Volke; Douglas McCloskey; Pablo Iván Nikel *New Biotechnology*
- [Nine quick tips for analyzing network data](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007434) Vincent Miele; Catherine Matias; Stéphane Robin; Stéphane Dray *PLOS Computational Biology*
- [Sharing biological data: why, when, and how](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14067) Samantha L. Wilson; Gregory P. Way; Wout Bittremieux; Jean-Paul Armache; Melissa A. Haendel; Michael M. Hoffman *FEBS Letters*
- [The role of ontologies in biological and biomedical research: a functional perspective](https://academic.oup.com/bib/article/16/6/1069/226068?login=false) Robert Hoehndorf; Paul N. Schofield; Georgios V. Gkoutos *Briefings in Bioinformatics*
- [The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](https://www.nature.com/articles/nbt1346) Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; ...; Richard H Scheuermann, Nigam Shah, Patricia L Whetzel & Suzanna Lewis *Nature Biotechnology*