Creation of an open, Open Medicinal Chemistry Course #416

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alintheopen opened this Issue Jul 13, 2016 · 19 comments

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alintheopen commented Jul 13, 2016

Undergraduate laboratory classes at MCPHS (@MedChemProf), Haverford College (@rbroadrup-HC), Lawrence University (@sdebbert) and USyd have participated in the synthesis of OSM molecules. Additionally, @PatrickThomson has supervised a number of project students in the lab at Edinburgh University (@jamiescott11 et al) and @murrayfold, Paul Ylioja and myself have had the pleasure of working with UG volunteers, honours (@JimCronshaw, @JoannaUbels and @tscmacdonald) and PhD students (@edwintse) at USyd.

In an online meeting yesterday, @rbroadrup-HC and some of his students mentioned that they would be interested in integrating some Medicinal Chemistry modules to compliment their laboratory course. This got us all thinking about how we might produce an open course on Open Medicinal Chemistry. Some topics would be common to all med chem courses and some would be coloured by our experiences of working openly. I can see many applications of this course and really like the idea that students can both contribute and consume the educational material produced.

Firstly, we should check to see what's already out there. For example @drc007 authors a fantastic website with many great resources (for example, this article on solubility
and then I think we should think about:

  • who might be interested in contributing
  • how we could best keep the materials together and 'editable' and open
  • which topic areas we'd like to cover
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@alintheopen Please count me in to help with this great idea. In addition to the OSM project, I have been working on using some software based early drug discovery simulations (starting with some of the open source malaria screening data.) The lab exercise is being used by first year Pharmaceutics or Pharmacology graduate students. I will be speaking about this at the upcoming ACS meeting in August.

I have been having the students use a software package known as StarDrop by Optibrium. Not open source, but the company has been very generous with the software for purely educational purposes. I am more than happy to package up all of my materials and share with the group.

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MedChemProf commented Jul 13, 2016

@alintheopen Please count me in to help with this great idea. In addition to the OSM project, I have been working on using some software based early drug discovery simulations (starting with some of the open source malaria screening data.) The lab exercise is being used by first year Pharmaceutics or Pharmacology graduate students. I will be speaking about this at the upcoming ACS meeting in August.

I have been having the students use a software package known as StarDrop by Optibrium. Not open source, but the company has been very generous with the software for purely educational purposes. I am more than happy to package up all of my materials and share with the group.

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👍 awesome Chase. If you are able to share your slides after the talk that would be great too.

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alintheopen commented Jul 13, 2016

👍 awesome Chase. If you are able to share your slides after the talk that would be great too.

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Of course. I will post once they are finalized.

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MedChemProf commented Jul 13, 2016

Of course. I will post once they are finalized.

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Small side question: How would I be able to get stardrop for free? How would I prove I am with osm?

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MFernflower commented Jul 13, 2016

Small side question: How would I be able to get stardrop for free? How would I prove I am with osm?

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drc007 Jul 14, 2016

I'd be happy to contribute, in particular I'd be more than willing to make additions to the Drug Discovery Resources section on my website (http://www.cambridgemedchemconsulting.com/resources/) such they can be used to provide online support for any MedChem Course.
@alintheopen I have a large number of slides I could contribute, but I assume you would need to decide on an open source software presentation application.

drc007 commented Jul 14, 2016

I'd be happy to contribute, in particular I'd be more than willing to make additions to the Drug Discovery Resources section on my website (http://www.cambridgemedchemconsulting.com/resources/) such they can be used to provide online support for any MedChem Course.
@alintheopen I have a large number of slides I could contribute, but I assume you would need to decide on an open source software presentation application.

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drc007 Jul 14, 2016

@MFernflower @MedChemProf I suspect Optibrium might view a student using Stardrop for a month or two as part of their course differently to long term use. You would need to contact them directly. An alternative might be to use DataWarrior (http://www.openmolecules.org/datawarrior/)

drc007 commented Jul 14, 2016

@MFernflower @MedChemProf I suspect Optibrium might view a student using Stardrop for a month or two as part of their course differently to long term use. You would need to contact them directly. An alternative might be to use DataWarrior (http://www.openmolecules.org/datawarrior/)

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alintheopen Jul 14, 2016

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Thanks Chris!

On Thu, Jul 14, 2016 at 6:05 PM, Chris Swain notifications@github.com
wrote:

@MFernflower https://github.com/MFernflower @MedChemProf
https://github.com/MedChemProf I suspect Optibrium might view a student
using Stardrop for a month or two as part of their course differently to
long term use. You would need to contact them directly. An alternative
might be to use DataWarrior (http://www.openmolecules.org/datawarrior/)


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alintheopen commented Jul 14, 2016

Thanks Chris!

On Thu, Jul 14, 2016 at 6:05 PM, Chris Swain notifications@github.com
wrote:

@MFernflower https://github.com/MFernflower @MedChemProf
https://github.com/MedChemProf I suspect Optibrium might view a student
using Stardrop for a month or two as part of their course differently to
long term use. You would need to contact them directly. An alternative
might be to use DataWarrior (http://www.openmolecules.org/datawarrior/)


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@MFernflower I think it is a little early to worry about getting a particular software package. I just mentioned it since that was the one that I am using. I think once the course that @alintheopen is suggesting takes some shape, then the discussion can follow.

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MedChemProf commented Jul 14, 2016

@MFernflower I think it is a little early to worry about getting a particular software package. I just mentioned it since that was the one that I am using. I think once the course that @alintheopen is suggesting takes some shape, then the discussion can follow.

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MFernflower commented Jul 14, 2016

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@alintheopen perhaps someone could host a dedicated wiki to the course - (I might help write a bit of it - depending on how things go

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MFernflower commented Jul 19, 2016

@alintheopen perhaps someone could host a dedicated wiki to the course - (I might help write a bit of it - depending on how things go

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Canute201 Jul 20, 2016

Hi, this looks like a very interesting initiative. In terms of some things that are already out there, this from edX looks potentially interesting, though it looks like you need to sign up (free I think) to find out very much more:

https://www.edx.org/course/medicinal-chemistry-molecular-basis-drug-davidsonx-d001x-1

Hi, this looks like a very interesting initiative. In terms of some things that are already out there, this from edX looks potentially interesting, though it looks like you need to sign up (free I think) to find out very much more:

https://www.edx.org/course/medicinal-chemistry-molecular-basis-drug-davidsonx-d001x-1

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@Canute201 It's a free course - I'm watching some videos on lead optimization right this moment

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MFernflower commented Jul 20, 2016

@Canute201 It's a free course - I'm watching some videos on lead optimization right this moment

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drc007 Sep 8, 2016

@alintheopen @MedChemProf @rbroadrup-HC I've spoken to a few people about this and there is certainly an interest in developing/contributing to such a resource. It might be useful to brainstorm around what we want to include. Would it be simply slide decks, videos of lectures and webinars, links to online reading resources, hints, how to descriptions? How would these be maintained/updated?

drc007 commented Sep 8, 2016

@alintheopen @MedChemProf @rbroadrup-HC I've spoken to a few people about this and there is certainly an interest in developing/contributing to such a resource. It might be useful to brainstorm around what we want to include. Would it be simply slide decks, videos of lectures and webinars, links to online reading resources, hints, how to descriptions? How would these be maintained/updated?

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Apologies for not replying on this one - am taking observer status at the
moment - but I guess my initial question would be: are you thinking of a
static set of bundled resources, or are you thinking of something less
bounded, like across-the-board improvement of wiki articles? Or something
in between? If you're thinking of anything other than Wikipedia, then a
dull resources question raises its ugly head - who will accept
responsibility for managing the resources you make, both during creation
and into the future? If you want people to contribute as you go (a real
strength) then the resources need to be public domain, as per the ELNs we
use. There are solutions - there just needs to be a very general outline
agreement amongst contributors.

On 8 September 2016 at 23:28, Chris Swain notifications@github.com wrote:

@alintheopen https://github.com/alintheopen @MedChemProf
https://github.com/MedChemProf @rbroadrup-HC
https://github.com/rbroadrup-HC I've spoken to a few people about this
and there is certainly an interest in developing/contributing to such a
resource. It might be useful to brainstorm around what we want to include.
Would it be simply slide decks, videos of lectures and webinars, links to
online reading resources, hints, how to descriptions? How would these be
maintained/updated?


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mattodd commented Sep 12, 2016

Apologies for not replying on this one - am taking observer status at the
moment - but I guess my initial question would be: are you thinking of a
static set of bundled resources, or are you thinking of something less
bounded, like across-the-board improvement of wiki articles? Or something
in between? If you're thinking of anything other than Wikipedia, then a
dull resources question raises its ugly head - who will accept
responsibility for managing the resources you make, both during creation
and into the future? If you want people to contribute as you go (a real
strength) then the resources need to be public domain, as per the ELNs we
use. There are solutions - there just needs to be a very general outline
agreement amongst contributors.

On 8 September 2016 at 23:28, Chris Swain notifications@github.com wrote:

@alintheopen https://github.com/alintheopen @MedChemProf
https://github.com/MedChemProf @rbroadrup-HC
https://github.com/rbroadrup-HC I've spoken to a few people about this
and there is certainly an interest in developing/contributing to such a
resource. It might be useful to brainstorm around what we want to include.
Would it be simply slide decks, videos of lectures and webinars, links to
online reading resources, hints, how to descriptions? How would these be
maintained/updated?


You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#416 (comment),
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.

MATTHEW TODD | Associate Professor
School of Chemistry | Faculty of Science

THE UNIVERSITY OF SYDNEY
Rm 519, F11 | The University of Sydney | NSW | 2006
T +61 2 9351 2180 | F +61 2 9351 3329 | M +61 415 274104
E matthew.todd@sydney.edu.au | W
http://sydney.edu.au/science/people/matthew.todd.php
W http://opensourcemalaria.org/ | W http://opensourcetb.org/ | W
http://opensourcepharma.net/

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Jake-s16 Dec 1, 2016

Don't know how relevant this is but have you seen http://www.chem1.com/acad/webtext/virtualtextbook.html Terms of use: Creative Commons Attribution 3.0 License.

Jake-s16 commented Dec 1, 2016

Don't know how relevant this is but have you seen http://www.chem1.com/acad/webtext/virtualtextbook.html Terms of use: Creative Commons Attribution 3.0 License.

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rajasgodbole Dec 9, 2016

Id be happy to enroll i had basic medicinal chemistry for last semester of my undergrad year but devil is in the details !
Lets Enroll !!

Id be happy to enroll i had basic medicinal chemistry for last semester of my undergrad year but devil is in the details !
Lets Enroll !!

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mcoster Oct 3, 2017

Hey all, I just (re?)discovered this issue and it's right in line with some of my recent interests. Nice thread @alintheopen @mattodd @MedChemProf @drc007 and others.

Having discovered the wonders of open source science through OSM, I've been seeing the world through much more open eyes (hah!). In combination with adopting some more modern teaching techniques (eg. high structure, active learning), I wanted to open up my teaching materials. The more I think about it, the more frustrating it is that we all put so much effort into developing these things that get cloistered away. My eventual goal is to have the majority of my teaching content available in an open format, and for my face-to-face role at my home institution to be centred on learning facilitation, accreditation, lab components, etc.

My first foray, this term just ended, was a very short section on "Synthesis in Drug Design" in a course titled Drug Design & Delivery. For this, I set up a "Course Hub" website using the open-source flat-file CMS, Grav. One of the main reasons I went this route is because of the great Grav Course Hub Skeleton, developed by @paulhibbitts - a very Open Ed friendly UX designer and educator. It is such a great resource for open/collaborative educators:

  • content is Markdown based
  • uses Git Sync - eg. content can be synced with GitHub, and edits can be managed via
  • Paul has similar Open Educational Resources (OER) and Open Publishing Space skeletons
  • content can be set out in a more controlled, user-friendly manner than a wiki (my opinion)

I ran into a a couple of obstacles in implementing my course hub:

  1. I simply ran out of time - learning a new CMS, developing new content and implementing a bunch of other course changes at the same time was very time-consuming
  2. Significant portions of my previously developed content was ok for internal use, from a fair use standpoint, but not suitable for publishing on an open site with CC-BY type license.

My aim was to transfer content across to a non-course specific MedChem open ed resource at the end of the term. There isn't much to transfer at the moment, but stumbling on this Issue has me thinking about how best to go forward.

So, the bottom line is - if there is still interest, I would be keen to get this ball rolling, and happy to set up and act as initial coordinator. If this is of interest, can others comment on what they see as use cases? Is it a course with a well-defined syllabus? Undergraduate or graduate level? What differentiates it from freely-available MOOC-style courses, like the one by Erland Stevens of Davidson College? Is there interest in adopting one of the GitHub-synced, open source Grav skeletons by Paul Hibbitts?

Mark

mcoster commented Oct 3, 2017

Hey all, I just (re?)discovered this issue and it's right in line with some of my recent interests. Nice thread @alintheopen @mattodd @MedChemProf @drc007 and others.

Having discovered the wonders of open source science through OSM, I've been seeing the world through much more open eyes (hah!). In combination with adopting some more modern teaching techniques (eg. high structure, active learning), I wanted to open up my teaching materials. The more I think about it, the more frustrating it is that we all put so much effort into developing these things that get cloistered away. My eventual goal is to have the majority of my teaching content available in an open format, and for my face-to-face role at my home institution to be centred on learning facilitation, accreditation, lab components, etc.

My first foray, this term just ended, was a very short section on "Synthesis in Drug Design" in a course titled Drug Design & Delivery. For this, I set up a "Course Hub" website using the open-source flat-file CMS, Grav. One of the main reasons I went this route is because of the great Grav Course Hub Skeleton, developed by @paulhibbitts - a very Open Ed friendly UX designer and educator. It is such a great resource for open/collaborative educators:

  • content is Markdown based
  • uses Git Sync - eg. content can be synced with GitHub, and edits can be managed via
  • Paul has similar Open Educational Resources (OER) and Open Publishing Space skeletons
  • content can be set out in a more controlled, user-friendly manner than a wiki (my opinion)

I ran into a a couple of obstacles in implementing my course hub:

  1. I simply ran out of time - learning a new CMS, developing new content and implementing a bunch of other course changes at the same time was very time-consuming
  2. Significant portions of my previously developed content was ok for internal use, from a fair use standpoint, but not suitable for publishing on an open site with CC-BY type license.

My aim was to transfer content across to a non-course specific MedChem open ed resource at the end of the term. There isn't much to transfer at the moment, but stumbling on this Issue has me thinking about how best to go forward.

So, the bottom line is - if there is still interest, I would be keen to get this ball rolling, and happy to set up and act as initial coordinator. If this is of interest, can others comment on what they see as use cases? Is it a course with a well-defined syllabus? Undergraduate or graduate level? What differentiates it from freely-available MOOC-style courses, like the one by Erland Stevens of Davidson College? Is there interest in adopting one of the GitHub-synced, open source Grav skeletons by Paul Hibbitts?

Mark

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drc007 Oct 4, 2017

Another option would be iTunes University, for examples see.
https://www.harvard.edu/itunes
http://www.open.edu/itunes/
https://www.ox.ac.uk/itunes-u?wssl=1

This is already a vast resource and my children certainly used to do revision by rewatching lectures. The advantage is perhaps they can view all the lectures from all courses in one place.

drc007 commented Oct 4, 2017

Another option would be iTunes University, for examples see.
https://www.harvard.edu/itunes
http://www.open.edu/itunes/
https://www.ox.ac.uk/itunes-u?wssl=1

This is already a vast resource and my children certainly used to do revision by rewatching lectures. The advantage is perhaps they can view all the lectures from all courses in one place.

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