6
$\begingroup$

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 in SynBioHub but we are not sure how best to go about it. The plasmids have been designed and now they are starting to be produced in batches, checked and finally transformed into Synechocystis to induce a single gene deletion by homologous recombination. During the project, we will have:

  • Stage 1 – the initial plasmids designs, waiting for production. They are worth sharing as the community could influence the production queue.
  • Stage 2 – the assembled plasmids. In some cases they will have different structure than initial designs from stage 1. If nothing else their description should reflect the status change to 'produced'.
  • Stage 3 – plasmids are verified by sequencing (also to check the barcodes are correct) and sequences attached.
  • Stage 4 – plasmids will be transformed into Synechocystis and checked by PCR to see if i) the target gene has been knocked out and ii) if the strain is segregated (i.e. all copies of the genome in the strain contain the gene deletion). This information should also be recorded with the description.

Our initial plan was:

  • Create a collection with initial designs (component definitions) Stage 1
  • As stage 2 progresses add new versions of udpated designs
  • Stage 3, 4 update plasmids descriptions (synbio desc or notes) and attach additional files (e.g. from sequencing).

However, our current understanding is the public collections are frozen so stage 2,3,4 cannot be accommodated.

We are seeking advice how to plan for sharing this resource and some clarifications.

  1. Is there a way of making collection readable by others without freezing its content?
  2. What operations are possible on public component definitions, can the free text descriptions/notes be updated or file attached?
  3. Can new component definitions or their versions be added to a published collection
  4. For 2) 3) who can perform these operations, the collection’s creator or SynBio curators?

Looking forward to input from SynBioHub community

$\endgroup$
2
  • $\begingroup$ Welcome. Typically we ask that questions only contain a single question. Can you please consider condensing your post down to a single question and/or asking the remaining question in a separate post. Thanks. $\endgroup$
    – user438383
    Mar 30 at 10:44
  • $\begingroup$ Knowing something about SynBioHub, I think this is well-answerable as one question, because it's all focused on its publication workflow. I'm not sure of the answers myself, but I'm going to try to get one of the folks who does know to answer. $\endgroup$
    – jakebeal
    Apr 2 at 12:00
9
$\begingroup$

There is a balancing act between allowing all edits, which defeats the purpose of having URIs point to static objects, and allowing no edits, which defeats the purpose of providing some updated information about an object. SynBioHub resolves this issue by allowing a limited amount of edits after publication. To answer your questions specifically:

  1. Yes, you can share objects by generating a share link OR adding another owner to an object. Sharing can be done by the original owner of the object.
  2. There are some mutable fields that any owner of the object can change, these include the description, notes, source, and references in the Details section. You can also add attachments.
  3. Yes, when you publish (Make Public) a new object or collection, you have the option of making it public into an existing collection OR a new collection. A person with curator privileges on the SynBioHub instance you are working on can perform this operation.
  4. Answered above.
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.