Questions tagged [sbol]

Used for questions regarding the "Synthetic Biology Open Language", which can be used to describe genetic circuits, function, experimental data, etc.

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Creating Experimental Components on SBOL

I am developing software to store experiments or studies using SBOL3. In the regular synthetic biology workflow we will find the experimental components Strain and Media. A safe way to implement them ...
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Practial Tools for Automating Wetlab robotics [closed]

Are there any tools that produce Robotics protocols (General or platform-specific) from a bio-design (Genbank, SBOL etc) that are practically used within the lab? I have looked at: Puppeteer - Doesn'...
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Using SBOL for lineages of recombinant DNA molecules and strains

I wonder about using The Synthetic Biology Open Language (SBOL) for a project involving the development of a web application to track the lineage of recombinant DNA molecules in a laboratory ...
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1answer
16 views

Encoding different DNAs in pySBOL3?

I want to encode two different DNAs using pySBOL3. First dna is an engineered region usually composed by a transcriptional unit (TU) or a set of TUs. The second is vector which is a basically a ...
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1answer
32 views

Is SBOL-VOWS operational?

Synthetic Biology Open Language's Visual Ontology Webservice docs have example URLs but they all return a github pages 404. EDIT: The SBOL-VOWS has site has been fixed but the section on the SBOL ...
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1answer
38 views

Does SBOL support timing and threshold value parameters?

Like the propagation delay and threshold value parameters in electronic circuits, does SBOL format support any such parameters/glyph to represent the propagation delay (time to trigger the output ...
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1answer
44 views

How to represent random sequence elements in SBOL?

In our lab, we work with synthetic biology components with partially random sequences (similar to work in directed evolution). So, for example, we have a plasmid design with several components, ...
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1answer
103 views

How to share a collection of sbol designs in SynBioHub

We currently work on a project that will generate a collection of recombinant plasmids targeting over 3500 genes of the cyanobacterium Synechocystis sp. PCC 6803. We would like to share these designs ...
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1answer
113 views

How to use SBOL (Synthetic Biology Open Language)?

One of my students is working on the development of a SynBio tool to design and represent genetic circuits in a standardized format. I know there are some libraries out there. What I am interested in ...
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2answers
84 views

Is there a good practice (or an easy one for a SBOL newbie) to set up a collection of biological parts and devices?

I have a collection of biological parts and devices in a particular format that basically stores information of the sequence of the elements. My intention is to move to a more standardized data ...
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1answer
78 views

In SBOL, is there a way to distinguish biological replicates?

I have a library of biological implementations (i.e. plasmids) of genetic circuits and their experimental data associated. I want to implement an in silico version with SBOL, but to be consistent with ...
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1answer
21 views

Can SBOL encode DNA Assembly linkers?

Where in an SBOL file could you specify the linkers that would be placed as prefixes / suffixes between parts for assembly? Lets say you have a final construct of your design and want to assemble the ...
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34 views

How do you represent small molecules in SBOL? [closed]

In SBOL, how do you represent small molecules like arabinose or chloramphenicol? There's a type for saying a component is a small molecule, but they don't really have sequences like DNA or proteins ...
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2answers
44 views

Why does SBOL have both Component and ComponentDefinition?

What is the point of having both a Component and a ComponentDefinition in SBOL? Shouldn't you be able to link straight from one component to its sub-components? The same question goes for Module and ...
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1answer
43 views

Does SBOL require representing intermediate products like mRNA?

Do I need to include intermediate gene products like mRNA in order to express a gene regulatory relationship in SBOL? For example, let's say that I'm representing transcriptional regulation of the ...
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1answer
38 views

In SBOL, when should I annotate a DNA sequence vs. making sub-components?

When representing a DNA sequence in SBOL as a ComponentDefinition, you can mark things like promoters and coding sequences in two different ways: either as a ...