Make Notebook 01 more like Chemistry Toolkit Rosetta

[mnowotka]

There is a Chemistry Toolkit Rosetta Wiki, which is a very valuable resource, comparing chemistry toolkit. Since we already have RDkit, OpenBabel and Indigo on board, we can include some of the stuff presented there in our introductory Notebook.

In the introduction notebook, we should put as much references to other notebooks as well to attract the user. Examples may contain for example retrieving data from ChEMBL using raw SQL, ORM, raw REST calls, client.

[flatkinson]

I would be cautious about introducing material using other toolkits without a strong rationale. If we need to use other toolkits behind the scenes (e.g. Indigo for depictions), that's fine, but I'd vote to keep the focus on RDKit for public-facing stuff.

[mnowotka]

Why?

On Fri, Oct 17, 2014 at 9:15 AM, flatkinson notifications@github.com
wrote:

I would be cautious about introducing material using other toolkits
without a strong rationale. If we need to use other toolkits behind the
scenes (e.g. Indigo for depictions), that's fine, but I'd vote to keep the
focus on RDKit for public-facing stuff.

—
Reply to this email directly or view it on GitHub
#9 (comment).

[flatkinson]

OK: I, personally (YMMV /etc/.), prefer to focus on one toolset. In the
past I've been in the situation of needing to mix and match
cheminformatics tools and toolkits (Daylight + MDL + Tripos most
notably, with MOE, Schrodinger, Accelrys, OpenBabel and ChemAxon stuff
introduced along the way) and it usually leads to pain in the end, due
to different chemistry models, assumptions /etc/. Of course, there are
always cases where you really have to work with multiple tools at once,
but generally I think you're better off focussing on one, even where
it's sometimes slightly suboptimal.

Also, fragmentation can be a problem in this field, and it's important
to keep up momemtum behind a project. I'd rather see us 'partner with
RDKit', if you like, and see if we can help it move forward. In fact, we
could approach Greg and see what he'd think of bundling his tutorial
material with myChEMBL, so people can give them a go (/e.g./ via
notebooks) before they invest time in installing the beast (installation
not being it's best feature).

We should also make sure as much of the forthcoming drug-design course
material is myChEMBL compatible, so people can take it away and re-run
it offline without problems.

On 17/10/2014 09:27, Michał Nowotka wrote:

Why?

On Fri, Oct 17, 2014 at 9:15 AM, flatkinson notifications@github.com
wrote:

I would be cautious about introducing material using other toolkits
without a strong rationale. If we need to use other toolkits behind the
scenes (e.g. Indigo for depictions), that's fine, but I'd vote to
keep the
focus on RDKit for public-facing stuff.

—
Reply to this email directly or view it on GitHub
#9 (comment).

—
Reply to this email directly or view it on GitHub
#9 (comment).

Dr Francis L Atkinson

Chemogenomics Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

(01223) 494473

[mnowotka]

Comparing RDKit to other toolkits doesn't mean we are not focusing on RDKit. I'm not proposing to mix different libraries in our software stack - in fact we use RDKit almost exclusively and this is not going to change. But I can imagine that people using my_chembl can have different backgrounds so a quick guide of how to achieve the same functionality using RDKit can be helpful.