ChemWiki - User contributions [en]

ILabber

2012-03-30T13:42:00Z

Ab7511: /* Please contribute below */

= iLabber Trial =

== Launch ==
Dear all,

You will have all received a login password for iLabber.

I queried the lack of any pre-built templates with Accelrys, and received this reply "Dear Prof. Rzepa, I checked with my colleagues from support. There are no default templates in iLabber, this allows flexibility to create own templates from the sections offered. However you can ask other coordinators from the iLabber pilot to send you a PDF of a template to see what sections they are using for Computational Chemistry experiments. If you need further information please do not hesitate to contact me." I have to admit that I have not yet been "trained" in the art of creating a project template, and Richard Whitby tells me that "Given the functionality I am not sure how important pre-defiend templates will be(though we are trying to produce an excel based one to accelerate entry of safety data)".

I would like everyone on this pilot to look through the features of iLabber, and consider how they might use the functionality for their own lab work. If you find the process difficult, record that as well. It might be a good idea if we all met in person to discuss the first few weeks experience of the system. Already I find the Help pages rather minimalist. Indeed, perhaps having an expert actually demonstrate the system might be a help.

There are many ways in which we could keep a local account of experiences, hints, etc. We could start by repeating how we documented the earlier MnovaDB trial, by going to https://wiki.ch.ic.ac.uk/wiki/index.php?title=ILabber and depositing your thoughts there. I have already been asked to complete a survey of the national project, at https://www.isurvey.soton.ac.uk/4882/36830/8Q9F6A/Imperial+College+London to document how we found the start of the project

and there is also an invitation to join a Google groups forum at http://groups.google.com/group/ilabber-uk-academic-pilot/sub?s=1ednLBQAAADwPLnPNldBKZy0eNokB47rTs88g-WnFbb4C853MSmguA&hl=en-GB (which may be email specific). These requests could easily become intrusive, and so we should strive to keep them to a minimum. I hope however that this email is not quite in that category!--[[User:Rzepa|Rzepa]] 17:22, 23 March 2012 (UTC)

----

I've had 2 attempts at using iLabber. One failed at the first step with an error message that my office PC software is not compatible with iLabber " iLabber does not run on this browser/computer combination"

My first attempt on my Mac Airbook was more successful in logging on and creating a new project and experiment. The snag here was that iLabber can't see that I have ChemDraw installed. I have the option to install MarvinDraw with the threat that I will need to upgrade to iLabber Premium in 2 weeks time. With a four day college closure during the next 2 weeks, this could be a short trial unless we can be upgraded.

Andy

Mnova DB trial

2012-01-10T09:23:47Z

Ab7511:

= MNovaDB Trial =

== '''Participants''' ==

Tim Barrett

Andy Bell

Paul Dingwall

Tom McCarthy-Ward

Adi Nako

'''Links'''

http://mestrelab.com/software/mnova-db/

http://mestrelab.com/downloads/manuals/MestReNova-7.1.0_Manual.pdf

Server:

Currently set up on a standard dc7800 desktop in room 135b called ch-mnovadb

Running under an instance of MySQL using locally created user names

I can see how to save the data to the NMR database but not how to attach structures. Any hints? It's alos not obvious how to link NMR spectra to lab book page numbers, which appear on the spectra.

Otherwise the trial is OK.

---------------------------

I think the idea is you create a document in Mnova then save it to the database.

A Document has a number of Pages. When you run up Mnova you get a blank sheet and a small copy of it at the top left hand side

From the edit menu you'll see "insert object" with a selection of formats including Chemdraw and chem3d.

Once you've do that you can do "create new page" and add your spectrum and so on.

The do the same again and add text eg recipe for making substance, references, physical data, Origin plots or whatever you like

You can then save the whole as a document either standalone or to the database.

I'll admit to not RTFM so there may be another way....

I

Hope this helps

[[User:Nd01|Nd01]] 09:58, 21 December 2011 (UTC)Nick

I'd tried this way but it didn't seem to recognise the structure as a molecule. I looked into the database structure and saw that it's looking for a mol file. So saved the ChemDraw structure as a mol file, copy and paste and it works.Hopefully the structures will be searchable.

As noted above, the key is whether the entries are sub-structure searchable. --[[User:Rzepa|Rzepa]] 13:50, 6 January 2012 (UTC)

== Bruker Alternative ==

here are several Bruker products under the banner heading CMC (for complete molecular confidence). The one I took most interest in was a very elegant tool for automatic assignment which could be linked to a structure.

In answer to Henry's question, I've just worked out how to carry out sub-structure searches. Hurray! You can also search by molecular formula.The structure and sub-structure search options are "greyed" out when looking at the database. Save your substructure as a mol file, copy and paste onto a spare spectrum and while highlighted, the structure searching options appear. The results tell you which entries contain the substructure. I haven't worked out how to look at the individual compounds other than by going back to the appropriate record. [[User:Ab7511|Ab7511]] 09:23, 10 January 2012 (UTC)

Mnova DB trial

2011-12-21T10:23:41Z

Ab7511:

'''Participants'''

Tim Barrett

Andy Bell

Paul Dingwall

Tom McCarthy-Ward

Adi Nako

'''Links'''

http://mestrelab.com/software/mnova-db/

http://mestrelab.com/downloads/manuals/MestReNova-7.1.0_Manual.pdf

Server:

Currently set up on a standard dc7800 desktop in room 135b called ch-mnovadb

Running under an instance of MySQL using locally created user names

I can see how to save the data to the NMR database but not how to attach structures. Any hints? It's alos not obvious how to link NMR spectra to lab book page numbers, which appear on the spectra.

Otherwise the trial is OK.

---------------------------

I think the idea is you create a document in Mnova then save it to the database.

A Document has a number of Pages. When you run up Mnova you get a blank sheet and a small copy of it at the top left hand side

From the edit menu you'll see "insert object" with a selection of formats including Chemdraw and chem3d.

Once you've do that you can do "create new page" and add your spectrum and so on.

The do the same again and add text eg recipe for making substance, references, physical data, Origin plots or whatever you like

You can then save the whole as a document either standalone or to the database.

I'll admit to not RTFM so there may be another way....

I

Hope this helps

[[User:Nd01|Nd01]] 09:58, 21 December 2011 (UTC)Nick

I'd tried this way but it didn't seem to recognise the structure as a molecule. I looked into the database structure and saw that it's looking for a mol file. So saved the ChemDraw structure as a mol file, copy and paste and it works.Hopefully the structures will be searchable.

Mnova DB trial

2011-12-21T09:37:40Z

Ab7511:

User talk:Ab7511

2011-12-21T09:36:12Z

Ab7511: Created page with "I can see how to save the data to the NMR database but not how to attach structures. Any hints? It's also not obvious how to link NMR spectra to lab book page numbers, which ap..."

I can see how to save the data to the NMR database but not how to attach structures. Any hints? It's also not obvious how to link NMR spectra to lab book page numbers, which appear on the spectra.

Otherwise the trial is OK.