Answers.Body: <p>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:</p>
  <ol>
  <li>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.</li>
  <li>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.</li>
  <li>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.</li>
  <li>Answered above.</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-02T17:11:27.007Z
Answers.LastActivityDate: 2021-04-02T17:11:27.007Z
Answers.UserDisplayName: Chris Myers
Body: <p>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:</p>
  <ul>
  <li>Stage 1 – the initial plasmids designs, waiting for production. They
  are worth sharing as the community could influence the production
  queue.</li>
  <li>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'.</li>
  <li>Stage 3 – plasmids are verified by sequencing (also to
  check the barcodes are correct) and sequences attached.</li>
  <li>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.</li>
  </ul>
  <p>Our initial plan was:</p>
  <ul>
  <li>Create a collection with initial designs (component definitions) Stage 1</li>
  <li>As stage 2 progresses add new versions of udpated designs</li>
  <li>Stage 3, 4 update plasmids descriptions (synbio desc or notes) and attach additional files (e.g. from sequencing).</li>
  </ul>
  <p>However, our current understanding is the public collections are frozen so stage 2,3,4 cannot be accommodated.</p>
  <p>We are seeking advice how to plan for sharing this resource and some clarifications.</p>
  <ol>
  <li>Is there a way of making collection readable by others without freezing its content?</li>
  <li>What operations are possible on public component definitions, can the free text descriptions/notes be updated or file attached?</li>
  <li>Can new component definitions or their versions be added to a published collection</li>
  <li>For 2) 3) who can perform these operations, the collection’s creator or SynBio curators?</li>
  </ol>
  <p>Looking forward to input from SynBioHub community</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-30T10:44:17.027Z
Comments.Text: 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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-04-02T12:00:04.380Z
Comments.Text: 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.
Comments.UserDisplayName: jakebeal
Tags: <sbol>
Title: How to share a collection of sbol designs in SynBioHub
ThreadText: # How to share a collection of sbol designs in SynBioHub
  
  (Asked by: username_0 on 2021-03-29)
  
  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
  
  **Tags:** sbol
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: 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.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2021-04-02. Score: 9 | Accepted answer
  
  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.
  
  
  ---
  
  