Discussion:
[BlueObelisk-discuss] Molecular Craigslist
Peter Murray-Rust
2012-07-06 16:52:18 UTC
Permalink
Mat Todd has raised the exciting idea of a Craigslist for molecules - "I
would like some of *this*". His post is at
http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/

We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would be
very welcome. Since many would be new molecules (and presumably organic) we
can use InChI but we need a nice Open interface. We'll be looking at some
of the latest OKF tools and maybe they will create most of what is
necessary.

Do we have a JS-enabled molecular viewer for InChIs, for example to embed
in web pages?
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Wolf Ihlenfeldt
2012-07-06 17:24:02 UTC
Permalink
Are you aware of Innocentive (www.innocentive.com) ? They have been
operating for many years. OK, they are commercial, but backed by many
chemistry/life science companies...
Post by Peter Murray-Rust
Mat Todd has raised the exciting idea of a Craigslist for molecules - "I
would like some of *this*". His post is at
http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/
We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would
be very welcome. Since many would be new molecules (and presumably organic)
we can use InChI but we need a nice Open interface. We'll be looking at
some of the latest OKF tools and maybe they will create most of what is
necessary.
Do we have a JS-enabled molecular viewer for InChIs, for example to embed
in web pages?
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Peter Murray-Rust
2012-07-06 17:46:24 UTC
Permalink
Post by Wolf Ihlenfeldt
Are you aware of Innocentive (www.innocentive.com) ? They have been
operating for many years. OK, they are commercial, but backed by many
chemistry/life science companies...
Yes - Mat mentioned innocentive in his mail.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
richard apodaca
2012-07-07 21:35:58 UTC
Permalink
Hello Peter,
 Do we have a JS-enabled molecular viewer for InChIs, for example to embed in web pages?
Interesting idea. To my knowledge, no. Noel offers a good start, though:

http://http://bit.ly/LVCsGK


Best,
Rich

---

blog: http://depth-first.com
company: http://metamolecular.com


________________________________
From: Peter Murray-Rust <***@cam.ac.uk>
To: BlueObelisk-Discuss <blueobelisk-***@lists.sourceforge.net>
Sent: Friday, July 6, 2012 9:52 AM
Subject: [BlueObelisk-discuss] Molecular Craigslist


Mat Todd has raised the exciting idea of a Craigslist for molecules - "I would like some of *this*". His post is at http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/

We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would be very welcome. Since many would be new molecules (and presumably organic) we can use InChI but we need a nice Open interface. We'll be looking at some of the latest OKF tools and maybe they will create most of what is necessary.

Do we have a JS-enabled molecular viewer for InChIs, for example to embed in web pages?
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Noel O'Boyle
2012-07-08 16:58:09 UTC
Permalink
You could use the Markus Sitzmann's Chemical Identifier Resolver,
which uses Cactvs on the backend. It provides InChI lookup and image
generation via a simple REST api.

e.g. http://cactus.nci.nih.gov/chemical/structure/InChI%3D1S/C2H3ClO/c1-2%283%294/h1H3/image
returns a GIF for InChI=1S/C2H3ClO/c1-2(3)4/h1H3

There are lots of option to control the image size, etc.

- Noel
Post by Peter Murray-Rust
Mat Todd has raised the exciting idea of a Craigslist for molecules - "I
would like some of *this*". His post is at
http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/
We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would be
very welcome. Since many would be new molecules (and presumably organic) we
can use InChI but we need a nice Open interface. We'll be looking at some of
the latest OKF tools and maybe they will create most of what is necessary.
Do we have a JS-enabled molecular viewer for InChIs, for example to embed in
web pages?
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Peter Murray-Rust
2012-07-08 18:30:53 UTC
Permalink
Post by Noel O'Boyle
You could use the Markus Sitzmann's Chemical Identifier Resolver,
which uses Cactvs on the backend. It provides InChI lookup and image
generation via a simple REST api.
e.g.
http://cactus.nci.nih.gov/chemical/structure/InChI%3D1S/C2H3ClO/c1-2%283%294/h1H3/image
returns a GIF for InChI=1S/C2H3ClO/c1-2(3)4/h1H3
There are lots of option to control the image size, etc.
Thanks. If we use services they have to be as Open as possible but I think
the NIH probably meets this.
Post by Noel O'Boyle
- Noel
Post by Peter Murray-Rust
Mat Todd has raised the exciting idea of a Craigslist for molecules - "I
would like some of *this*". His post is at
http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/
We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would
be
Post by Peter Murray-Rust
very welcome. Since many would be new molecules (and presumably organic)
we
Post by Peter Murray-Rust
can use InChI but we need a nice Open interface. We'll be looking at
some of
Post by Peter Murray-Rust
the latest OKF tools and maybe they will create most of what is
necessary.
Post by Peter Murray-Rust
Do we have a JS-enabled molecular viewer for InChIs, for example to
embed in
Post by Peter Murray-Rust
web pages?
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
------------------------------------------------------------------------------
Post by Peter Murray-Rust
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Blueobelisk-discuss mailing list
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--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Nina Jeliazkova
2012-07-09 06:03:27 UTC
Permalink
Post by Peter Murray-Rust
Mat Todd has raised the exciting idea of a Craigslist for molecules - "I
would like some of *this*". His post is at
http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/
We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would
be very welcome. Since many would be new molecules (and presumably organic)
we can use InChI but we need a nice Open interface. We'll be looking at
some of the latest OKF tools and maybe they will create most of what is
necessary.
Do we have a JS-enabled molecular viewer for InChIs, for example to embed
in web pages?
Ambit has depiction REST services, accepting InChI , SMILES or names (via
OPSIN) and returning PNG or GIF.

Links like this could be directly used in <img> tag, they return png

http://apps.ideaconsult.net:8080/ambit2/depict/cdk/any?search=InChI%3D1%2FC6H8O6%2Fc7-1-2%288%295-3%289%294%2810%296%2811%2912-5%2Fh2%2C5%2C7-10H%2C1H2%2Ft2-%2C5%2B%2Fm0%2Fs1

Note InChI has to be URL encoded.

And one could compare depictions by several tools (also accept InChI ,
SMILES or names, but support depends on the specific tool)
http://apps.ideaconsult.net:8080/ambit2/depict?search=InChI%3D1%2FC6H8O6%2Fc7-1-2%288%295-3%289%294%2810%296%2811%2912-5%2Fh2%2C5%2C7-10H%2C1H2%2Ft2-%2C5%2B%2Fm0%2Fs1&smarts=

Alternatively, one could just upload any molecule list to this or another
Ambit [1] instance of his choice and built an appropriate GUI.

Best regards,
Nina

[1] http://ambit.sourceforge.net/pubs_citeambit.html
Post by Peter Murray-Rust
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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