any media object additions for media editor?

[nconrad]

@cshenry , @janakagithub, @jplfaria , @samseaver. It may be a good time to get all the data we need for editing media into the media objects. Can we have the compound names added? I think it makes sense to have the names readily available, particularly if custom compounds will be supported? Anything else? Charge? Below is all the data I have right now.

[jplfaria]

Compound names are essential. People will want to search for compound names, not IDs.

[cshenry]

Don�t need charge, but name makes alot of sense. I can add that.

On Jun 1, 2015, at 4:05 PM, jplfaria notifications@github.com wrote:

Compound names are essential. People will want to search for compound names, not IDs.

� Reply to this email directly or view it on GitHub.

[janakagithub]

Yes, compounds should be searchable by their aliases and abbreviations.

Sent from my Google Nexus 5 Don�t need charge, but name makes alot of sense. I can add that.

On Jun 1, 2015, at 4:05 PM, jplfaria notifications@github.com wrote:

Compound names are essential. People will want to search for compound names, not IDs.

� Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ProbModelSEED/issues/5#issuecomment-107720916 .

[chian]

Can we add blank spot for pH when we need it? May come in handy at some point.

Sent from my iPhone

On Jun 1, 2015, at 5:44 PM, janakagithub notifications@github.com wrote:

Yes, compounds should be searchable by their aliases and abbreviations.

Sent from my Google Nexus 5 Don�t need charge, but name makes alot of sense. I can add that.

On Jun 1, 2015, at 4:05 PM, jplfaria notifications@github.com wrote:

Compound names are essential. People will want to search for compound names, not IDs.

� Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ProbModelSEED/issues/5#issuecomment-107720916 . — Reply to this email directly or view it on GitHub.

[cshenry]

I think it's already there, but if it's not, I'll add it.

Sent from my iPhone

On Jun 1, 2015, at 6:26 PM, chian notifications@github.com wrote:

Can we add blank spot for pH when we need it? May come in handy at some point.

Sent from my iPhone

On Jun 1, 2015, at 5:44 PM, janakagithub notifications@github.com wrote:

Yes, compounds should be searchable by their aliases and abbreviations.

Sent from my Google Nexus 5 Don�t need charge, but name makes alot of sense. I can add that.

On Jun 1, 2015, at 4:05 PM, jplfaria notifications@github.com wrote:

Compound names are essential. People will want to search for compound names, not IDs.

� Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ProbModelSEED/issues/5#issuecomment-107720916 . — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

[mdejongh]

It would be good to search using identifiers from other databases too, e.g., KEGG compound ids.

Matt

On Mon, Jun 1, 2015 at 8:08 PM, cshenry notifications@github.com wrote:

I think it's already there, but if it's not, I'll add it.

Sent from my iPhone

On Jun 1, 2015, at 6:26 PM, chian notifications@github.com wrote:

Can we add blank spot for pH when we need it? May come in handy at some point.

Sent from my iPhone

On Jun 1, 2015, at 5:44 PM, janakagithub notifications@github.com wrote:

Yes, compounds should be searchable by their aliases and abbreviations.

Sent from my Google Nexus 5 Don�t need charge, but name makes alot of sense. I can add that.

On Jun 1, 2015, at 4:05 PM, jplfaria notifications@github.com wrote:

Compound names are essential. People will want to search for compound names, not IDs.

� Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub < https://github.com/ModelSEED/ProbModelSEED/issues/5#issuecomment-107720916

. — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/ModelSEED/ProbModelSEED/issues/5#issuecomment-107750528 .

Matthew DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

[samseaver]

I think formula would be useful, even if its self-explanatory in many cases, it serves as a reminder of the quantity of individual elements that would be consumed.

[mmundy42]

@nconrad, what else do you need here? It wasn't clear to me what server method is being used for media editing.

[nconrad]

The media editor above was prototyping with KBase data. Here's an update on modelseed/patric media.

I added a list of Chris's public media and media tables to the site under biochemistry. Calling get object on one of these returns a string of a tab delimited table. It currently has:

• compound name
• compound id
• concentration
• min flux
• max flux

Next steps/questions.

1) @chian requests that pH is added 2) @mdejongh requests that KEGG compound ids are added 3) Where should we store user's media? /username/media? 4) Since the media table/object is simple and small, editing the workspace data should be fine here. Any other ideas? 5) How can the user select their own media for reconstruction? I was thinking of just adding a radio button in the form to switch between public and user's media. Sound good?