Getting rid of question mark warning flags under components

[sulli365]

How do get rid of the yellow warning flags under glyphs that are part of larger components?

These flags do not appear on isolated glyphs...see attached example.

Also while I'm here - is there a way to toggle whether or not the part names show up underneath their respective glyphs? Long names get cut off which is not very useful from a publication perspective...

[cjmyers]

The question marks indicate that no sequence has been assigned to the part. If you use SynBioHub to select a part with a sequence or manually add a sequence they will go away.

We don't have an option for changing the label formatting. Thanks for the suggestion, we will add this to our to do list. As a temporary fix, you can add a text box over top of the label, which if filled will cover the existing label and allow you to add your own.

[sulli365]

Thank you very much for responding! That's good to know about the warning flags. I don't have a Synbiohub account login to use so I will just enter some random letters for the sequences - I am more interested (at the moment) in using SBOL canvas to make nice looking circuit diagrams without having to spend hours in powerpoint. Yeah, I also figured I could just cover the labels with a white text box/hack it someway but wanted to see if there was a built in way to do this. Best, Sean Sullivan

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On Tue, Feb 22, 2022 at 11:27 AM cjmyers ***@***.***> wrote: The question marks indicate that no sequence has been assigned to the part. If you use SynBioHub to select a part with a sequence or manually add a sequence they will go away. We don't have an option for changing the label formatting. Thanks for the suggestion, we will add this to our to do list. As a temporary fix, you can add a text box over top of the label, which if filled will cover the existing label and allow you to add your own. — Reply to this email directly, view it on GitHub <#208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEUNAMB3HUMW6LBJS3PPFATU4O2P7ANCNFSM5PAALLGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Sean Sullivan* PhD Candidate Tufts University - Nair Lab <https://sites.tufts.edu/nairlab/>

[cjmyers]

SBH logins are easy to get, but I agree that using this for just diagrams is nice. Probably we should also have a feature to remove the warnings for images.

[sulli365]

Ok so I made a SynBioHub login to try and upload my designs to save them but I keep getting errors. This is after also getting errors trying to download the designs to my laptop. Really hoping I can save/load these designs without having to remake them every time. Should I make a post on the forum with the error messages I'm getting? Thanks, Sean

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On Wed, Feb 23, 2022 at 8:25 PM cjmyers ***@***.***> wrote: SBH logins are easy to get, but I agree that using this for just diagrams is nice. Probably we should also have a feature to remove the warnings for images. — Reply to this email directly, view it on GitHub <#208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEUNAMBROVM53623QPXRC3DU4WCHNANCNFSM5PAALLGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Sean Sullivan* PhD Candidate Tufts University - Nair Lab <https://sites.tufts.edu/nairlab/>

[zachsents]

Hey @sulli365 I'm working on debugging SBOLCanvas, did you happen to save the error message you received?

[sulli365]

No I did not unfortunately - I planned to then my computer restarted for updates and the design was lost. Should I remake it and respond to this thread with the error messages I was receiving and what I was doing when I received them? Thanks, Sean

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On Thu, Feb 24, 2022 at 5:50 PM Zach Sents ***@***.***> wrote: Hey @sulli365 <https://github.com/sulli365> I'm working on debugging SBOLCanvas, did you happen to save the error message you received? — Reply to this email directly, view it on GitHub <#208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEUNAMH3GAQEKFPF7Q36VNDU42Y3PANCNFSM5PAALLGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- *Sean Sullivan* PhD Candidate Tufts University - Nair Lab <https://sites.tufts.edu/nairlab/>

[zachsents]

Yes, that would be super helpful. I'm trying to reproduce the errors and having a hard time getting them intentionally.

[sulli365]

Ok sorry for the delay but here are a couple issues that are cropping up when I try to do various things using the following circuit (pasted as an image here): [image: image.png] Some of the error messages that I've received reference an SBOLstandard.org document that I just found. I may just not be in compliance with whatever rules the software needs me to follow, but there is no link to this document from SBOLcanvas itself...these (numerous) restrictions are not intuitive or stated anywhere within SBOLcanvas itself that I can find (including in the tutorial). There is no save button under the File menu. In the youtube tutorial I found for using SBOLcanvas, there is a save button (~7:50 of the following video - https://www.youtube.com/watch?v=bzV_Dsc3ri8). When I try to download the module as a SBOL2 type file I get the following error message: sbol-10405:Weak Validation Error: the elements property of a Sequence MUST be consistent with its encoding property. Reference: SBOL Version 2.3.0 Section 7.6 on Page 20 : https://sbolcanvas.org/id3_sequence I can tell that there is a problem with the sequence field of id3 promoter. Previously you said that you can get rid of the yellow flags beneath each module component by entering a sequence, so I entered 'a' in the sequence box to get around this. Nowhere does it show a box labeled 'elements' or 'encoding' for this glyph. I can see from page 20 of the SBOLstandard document that I need to somehow enter both a nucleotide sequence and the url: http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html but I can't tell where or how. I created both a login and a collection on SynBioHub.org but when I try to upload this module to the collection that I made I get the same error message. Previously I got a much longer error message (that I didn't save). Overall, it kind of seems like I would need to invest a lot more time into this to learn what makes an acceptable part entry, create all the entries on the SynBioHub website (?), and then come back and actually build the circuit. This is unfortunate - I think just being able to use the software to make publication quality genetic circuit images would be very useful (no more messing around in powerpoint forever) without needing to read extensive documentation. Best, Sean

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On Thu, Feb 24, 2022 at 6:28 PM Zach Sents ***@***.***> wrote: Yes, that would be super helpful. I'm trying to reproduce the errors and having a hard time getting them intentionally. — Reply to this email directly, view it on GitHub <#208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEUNAMFVQROSBAPRISENT4TU425JJANCNFSM5PAALLGQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- *Sean Sullivan* PhD Candidate Tufts University - Nair Lab <https://sites.tufts.edu/nairlab/>

[zachsents]

@sulli365 Thanks for the thorough response! I think you might be getting that error because you have an extra character in your sequence, like a space after the "a" or something like that. Double check that and it should solve your issue.

I agree the error messages are pretty intuitive, and these are being shown as a result of too few checks going on in the background as you draw your diagram. We're working on adding some better validation in the background so you never see any of these errors.

As for making publishable images, you should be able to export images even when the SBOL export is throwing errors, although I know this isn't ideal. Also, a workaround for the IDs being cut off is to add a text block with the full text you want to display, which you'll also have control over the size of.

Thanks for the feedback, always appreciated and keep it coming.