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OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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Creation of an open, Open Medicinal Chemistry Course #416

Open alintheopen opened 8 years ago

alintheopen commented 8 years ago

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:

MedChemProf commented 8 years ago

@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.

alintheopen commented 8 years ago

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

MedChemProf commented 8 years ago

Of course. I will post once they are finalized.

MFernflower commented 8 years ago

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

@drc007 @MedChemProf

drc007 commented 8 years ago

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 8 years ago

@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/)

alintheopen commented 8 years ago

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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MedChemProf commented 8 years ago

@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.

MFernflower commented 8 years ago

I understand - I've been useing a slew of free packages from the EPA and chemaxon alongside Balloon, JMoL and JChemPaint and a web service called XenoSite - Hopefully I will be able to make a complete list on my ELN sometime today

MFernflower commented 8 years ago

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

Canute201 commented 8 years ago

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

MFernflower commented 8 years ago

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

drc007 commented 8 years ago

@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?

mattodd commented 8 years ago

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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Jake-s16 commented 7 years ago

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.

MFernflower commented 7 years ago

Equalibrium part might be of use

rajasgodbole commented 7 years ago

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 !!

mcoster commented 7 years ago

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:

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

drc007 commented 7 years ago

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.