Max’s Mark2Cure talk at SDBUS, Birthday wishes for Bertrand, and more

Last Wednesday, our lead programmer (Max) was the guest speaker for the San Diego Bioinformatics User Series over at UCSD. We were thrilled to see a Mark2Curator show up for his talk (big shout out to TAdams), and understand that not everyone who wanted to attend could make it. Fortunately, we’ve recorded his presentation, and after editing it (to remove the excessive motion from my poor filming technique), we’ve finally made his talk available. The video processing is one reason why this newsletter was sent today rather than on Friday (when it should have been sent out.)

The other reason is that it’s Bertrand’s birthday! If you’re new to the Mark2Cure community, you might not be familiar with Bertrand Might, whose infectious grin graces our landing page. Bertrand’s birthday serves as a reminder of each unique NGLY1 child that has inspired Mark2Cure and of the rare disease community members who have joined the effort to make sense of the literature.

Read the full post here.

Max to speak about Mark2Cure at SDBUS

Happy Thanksgiving!


Thank you all for your contributions and feedback to Mark2Cure. Mark2Cure has changed so much since the beta experiment and it’s all thanks to you! The improvements in Mark2Cure would not have happened without your input.

Our Eeyarestatin doc set now has 1 completed quest and is 70% complete! Check out the network that’s starting to come out of it, and watch the network grow by helping complete the other quests!

View the full post here.

Mark2Cure citizen science volunteers finish off another 300 abstracts

The O-linked Glycosylation disorders doc set contained 195 abstracts, while the first misfolded and mitochondrial doc set had 105 abstracts. BOTH doc sets were completed this week by the citizen science participants of Mark2Cure. 300 abstracts is no laughing matter considering that each abstract was read and annotated by at least 15 different users. That’s 4500 doc annotation submissions!

With the completion of these two doc sets, we’ve opened two more doc sets. Our smallest set yet is about Eeyarestatin and is already halfway done!

If you’re curious how your contributions matter, take a good look at the annotation network for Eeyarestatin. Are you seeing just white space? That’s because the computer has no idea what’s in this doc set yet, and needs you to point out what in this doc set. Once a quest reaches 15 completions, the annotations for that quest will appear in the network. Help build the network by finishing a quest today!

View the full post here.

New feature just in time for Friday the 13th!

It’s Friday the 13th, and we have an exciting new feature to share with you! You will now be able to see the information that you’ve helped to extract for each group. When you go to your dashboard, click on any of the doc-set titles to view the doc-set’s page. You’ll see a description of that doc-set, the progress bar for that set, and the option to ‘Toggle Network.’

2015.11.13 mfold-all

View the full post here.

CDG doc set done!

Composed of ~483 abstracts, the CDG doc set was one of the largest sets in Mark2Cure’s Campaign for NGLY1. This set was completed sometime on Tuesday night (07/28) and is the second doc set to be completed by the Mark2Cure community (the first one being the Alacrima set).

While we work on preparing the next doc set for release, there are still two doc sets available right now to the Mark2Cure community, both of which are over 60% complete.

The FBX/Engase Set

FBX2 description
F-box protein 2 (FBX2) and endo-beta-N-acetylglucosaminidase (ENGASE) are two genes which were identified to be potentially relevant to NGLY1 deficiency. There are very few papers linked to these two genes; but they may hold valuable clues regarding other relevant topics to search. Help finish this set.

Read the entire post here.

Can it be done? Can we finish 15 quests this weekend?

New features and fixes: Earlier, we introduced the document-specific ‘talk pages’, without too much fanfare since we wanted to ensure that it was working properly. Now that we’ve seen a few users jump in and demonstrate that it seems to be working properly, we invite you all to discuss the annotations on the documents you’ve completed. Thank you, bill, klgmd, edward, derosa, and kagaku for trying out the talk pages and posting really useful suggestions, tips, and questions. We can’t tell you how to do every single document, else we’d have already done them! But, with your help, we can all learn and improve with every doc!

As many of you may have noticed, the pre-population of the annotations wasn’t working properly for the last few weeks. Fortunately, this issue has been fixed.

We’ve also added a quick difficulty rating for each doc-set as a whole. Naturally, each set will have a good mix of docs of different difficulty levels.

More here.

At 95% Complete, the CDG doc set is almost done

This has been a rather large doc set, so you’ve all been amazing in bringing it this far. With around 480 docs in this set, we expected that completing this set would take some time. As of today, only 19 of the 97 or so quests still remain to be completed! If you have some time this weekend, please help complete some of these quests. Every little bit helps.

As many of you may have noticed, the pre-population of the docs hasn’t been working lately. We’re not exactly sure what happened, but Max has been working on fixing the issue. Which raises a question in our mind:

Let us know! Additionally, we’ve been rolling out a new feature this week, which we’ll highlight in greater detail later on. If you haven’t been on Mark2Cure in the last few days, complete a quest or two and check it out!

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Mark2Cure’s CDG doc set is ~90% Complete, please help finish it

First of all, a big and warm welcome to the Mark2Curators who have joined us recently! We’re very excited to have you and look forward to interacting with you in the future. By participating in Mark2Cure, you’ve joined a really awesome group of people who use their intelligence for a great cause. For those of you who have been persistently pushing the CDG doc set closer to completion, THANK YOU! The CDG doc set would not be at ~90% completion without your efforts.

If you haven’t Marked2Cure in awhile, please help us! Just completing one quest will help us move closer towards completing this doc set.

As per our user survey of the most desired features, we’ve implemented a new search function in Mark2Cure so that your recent marking can be copy/pasted into a search browser on a new page. Try it out!

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Mark2Cure welcoming the awesome folks from DMNS

If you’ve never heard of Yo Pearl, the Science Girl, you are missing out! She is the super-cool, ultra-chic alter ego of Dr. Nicole Garneau (a super-cool, ultra-chic researcher/science advocate/educator/communicator) from the Denver Museum of Nature & Science. Over at the Denver Museum of Nature & Science, they do all sorts of exciting open participatory science that might whet your appetite…literally! The Museum is famous for its citizen science initiative exploring the genetics of taste and they have an amazing program which encourages people of all ages and educational levels to interact with science.

Dr. Garneau, who has pioneered a lot of the museum’s educational and outreach efforts in citizen science, contacted Mark2Cure when she saw a presentation by Ben at the first Citizen Science Association Conference in February. Since then we’ve been steadily improving Mark2Cure waiting for the day when it would be worthy of attention from Yo Pearl, the Science Girl. Happily, that day has come.

This post was originally written for Mark2Cure and can be viewed in its entirety here.