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5th September 2015 @ 04:35

At the end of July OSM announced our graphical abstract competition. We wanted a striking single image (that summed up the science and open methods employed in our work on series one) to accompany our upcoming publication.

The competition called for open submissions and we were delighted to receive two wonderful entries, which the judges (Justine Alltimes, John Overington, Javier Gamo, Mat Todd and Alice Williamson) struggled to choose between. Here goes...

First Prize

The judges felt that Viputheshwar Sitaraman's image displayed the science and open methodology in an extremely clear and attractive manner and effectively conveyed the essence of the paper in a single image.

Viputheshwar Sitaraman's image will be published as the graphical abstract for our next paper and he also wins $600 - Congratulations! Note that following the end of the competition, the winning entry was tweaked slightly to make it acceptable for submission to a journal alongside the paper. This version is attached (Revised Final Winner.psd and .jpg). Please use this version when discussing OSM.

Revised Final Winner.psd

Revised Final Winner.jpg

Second Prize

The judges also loved the beautiful entry by Merinda Jayne Ramage. This stunning image really illustrated the citizen science aspect of the project and the judges thought she captured the teamwork behind the science. OSM really look forward to using Merinda's image on some upcoming projects. Merinda wins $200.

A HUGE thank you to both Viputheshwar and Merinda - OSM were thrilled to receive work from two talented artists and we hope that this project is the first of many collaborations with artists. 

Licence: These images may be used with CC-BY attribution to this page and the name of the original artist.

Post orginally Authored by Alice Williamson

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23rd July 2015 @ 07:00

This past month I've had the opportunity to do some work in the lab with Alice Williamson. My aim was the workup of four compounds (SSP-1:4) synthesised in an undergraduate lab

SSP compounds

here's a short summary of what I was able to accomplish: 

SSP-1: Once the bulk of the original solvent was removed, we ran SSP-1 through a silica column. However 1H NMR data suggested that there was still some impurities in the product. We thus ran the product through a second column. 1H NMR data looks promising, but still under analysis.

SSP-2: SSP-2 was succesfully worked up, with promising 1H NMR data.

SSP-3: SSP-3 was also succesfully worked up with promising 1H NMR data.

SSP-4: Unfortunately due to time constraints I wasn't able to finish off the work up of SSP-4, I presume that it will be finished up by Alice however. 

Overall I really enjoyed my time in the lab, met some great people and just had a great experience. I would recommend this to anyone, especially to those doing undergraduate studies in related Science degrees.I would like to thank again Alice Williamson and Mat Todd for providing me with the opportunity and taking the time to help me out on the way. 

All the best,

Sebastien Dath

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9th June 2015 @ 02:35

Last semester at Sydney Uni, Alice Williamson created a new lab course in what's known as the "Special Studies Program" in Chemistry - high achieving undergrads who are given the freedom to try something new and challenging. Alice, working with Adam Bridgeman and Peter Rutledge in the School of Chemistry, designed a set of experiments based on where we're up to with the chemistry in OSM's Series 4 - a research project funded by the ARC and MMV.

The lab manual is openly available, and the students had to keep open lab notebooks. Here they are! I'm not sure there's ever been a lab class quite like it. Students engaged in real research, where everything is shared. We're now going to incorporate what they discovered into OSM itself.

Excitingly, I think this would scale. One can imagine lab courses based around current needs in any open source drug discovery and development project, meaning we could, with proper mentorship, bring to bear very large levels of skilled human resource to tackle actual project needs, with global coordination between cohorts. Undergrads in other countries have already contributed to OSM.

The students had to make short videos talking about any aspect of their project - they were given complete creative control. I had the pleasure of watching these during a showing in one of our lecture theatres last month - I was deeply impressed (and, occasionally, slightly disturbed). Here's the full playlist.

SSP OSM Playlist

These students have done a fantastic job, and Alice deserves enormous kudos for driving this through from scratch. Well done!

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15th November 2014 @ 22:05

OSM is now lucky enough to include chemists from Sydney Grammar School, who are making some much-needed molecules in Series 4. Alice already welcomed them on board here and here. Our intrepid explorers are Jason Chami, Evan Hockings, William Talbot, Sebastian Schwartz, Hugh Russell, James Kalas, James Manton-Hall, Andreas Orsmond, Mackenzie Shaw and Alex Su (ping @O_S_M if we've missed anyone, guys) They are working together, and the relevant reactions have codes with “SGS” in them.

These guys are making an important synthetic intermediate, shown below right, which can be used in a subsequent reaction to deliver new candidate antimalarials. This is a "divergent" pathway, since we can attach various groups to the Sydney Grammar compound to make a variety of molecules with the same chemistry.

Sydney Grammar School Target

The chemistry’s not easy, but with some precedent this year from Jo Ubels and Tom MacDonald, and inspiration and guidance from Alice Williamson, and expert tuition from their teachers Erin Sheridan and Trent Wallis, they should have a shot at this tricky chemistry. (If you're a student reading this and asking "Can I input?" the answer is "yes" - get in touch)

The route being pursued is nicely shown here, where the first step (SGS 1-1) is also described. The second step (SGS 2-1) was a condensation of a hydrazine with para-CN benzaldehyde, and an attempt was made in parallel using a pyridine aldehyde (SGS 3-1). As this chemistry grows, we're going to need to add it to the synthesis section of the wiki, as a summary of progress.

The chemistry’s not easy - this is certainly more difficult than the stuff that I was doing in high school. Great start, guys - we’re all rooting for you to be able to get to the end of the synthetic sequence! These molecules will be very useful, right now.


This post originally authored by Mat Todd

Strings for Google

ClC1=CN=CC(Cl)=N1 InChI=1S/C4H2Cl2N2/c5-3-1-7-2-4(6)8-3/h1-2H LSEAAPGIZCDEEH-UHFFFAOYSA-N

ClC1=CN=CC2=NN=C([Ar])N21 InChI=1S/C5H2ArClN4/c6-5-10-9-4-2-8-1-3(7)11(4)5/h1-2H JTBLVZJIEUOKIG-UHFFFAOYSA-N

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6th November 2014 @ 00:27

The OSM consortium are excited to have some new members to the team; some excellent chemists from Sydney Grammar School. Erin Sheridan and Trent Wallis are working with a group of twelve students to synthesise some building blocks for the Series 4 Triazolopyrazines.

The target compounds were decided following discussion on GitHub and the students are now ready to start on their synthese. Erin and Trent are going to create a separate lab book/blog as part of the consortium's ELN.

There will be more news to follow, hopefully from the students themeselves as they sign up for the ELN, GitHub and Twitter. So watch this space!

There will be prizes awarded to the students who maintain the best ELN, so look out for some great experimental descriptions, photographs, videos and more!


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