Tag Archives: GenoCAD

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

GenoCAD webinar this Thursday, March 27

GenoCAD_logoAlthough it’s already posted in our news feed, I just wanted to add a reminder about our upcoming webinar on GenoCAD: open-source computer-assisted design software for synthetic biology. You can see the time and registration details here:

Free “Introduction to GenoCAD” Webinar presented March 27th

If you want to download the slides beforehand (so you don’t have to write everything down), you can access the slides and slide handouts for the Introduction here: www.openhelix.com/GenoCAD

But in case you can’t make it for schedule reasons, you can still access the same materials from our web site on our GenoCAD suite pages. You can watch the video, download slides and handouts, and also try out the accompanying exercises.

There’s also a second tutorial with more advanced topics, and you can watch that video or access associated training materials for that version too: www.openhelix.com/genoCAD2

We’ll also leave this post open for questions from the webinar–if we don’t have time to get to the issues we’ll tackle them here. Or if you go off and try some things yourself, and come up with something else you want to know or get stuck, we’ll get you the answers or guidance.

If you are the type to want some publications to read to better understand the resource, be sure to check out the GenoCAD team’s page with many references that will help you to understand the foundations of the development and features, and their directions going forward.

Reference:
Wilson M.L., Hertzberg R., Adam L. & Peccoud J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD., Methods in enzymology, PMID:

Video Tips of the Week, Annual Review 2013 (part 2)

As you may know, we’ve been doing these video tips-of-the-week for SiX years now. We have completed or collected around 300 little tidbit introductions to various resources through this past year, 2013. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I (last week).

Annual Review VI, part 2:

July 2013:
July 3: Yeast genome? There is an app for that!
July 10: Atlas of Genomic Switches in Plants
July 17: Multi-image Genome viewer, MIG
July 24: Worm behavioral phenotypes database
July 31: GTR, Genetic Testing Registry

August 2013:
August 7: Gemini, exploration of genetic variation
August 14: DNA Subway
August 21: iPlant’s Discovery Environment
August 28: GenePattern

September 2013:
September 4: 3D Protein Structure Modeling
September 11: OntoMaton productivity app
September 18: LongevityMap and more Human Ageing Genomic Resources
September 25: NHGRI’s funding portfolio structure

October 2013:
October 2: A Lapse in Appropriations, Some Affects on Research
October 9: GenoCAD, computer-assisted design for synthetic biology
October 16: Mobile-device enabled tutorial suites
October 23: PATRIC Protein Family Sorter
October 30: VectorEditor

November 2013:
November 6: ENCODE @ Ensembl
November 13: Advanced Topics in GenoCAD
November 20: IGB, Integrated Genome Browser
November 27: Thanksgiving holiday break, but see Thanksgiving Genomes.

December 2013:
December 4:  Creating an Electronic Informed Consent
December 11: UCSC Track Hubs
December 18: CodersCrowd
December 25: Annual Tip Review part 1

Video Tips of the Week, Annual Review 2013 (part 1)

As you may know, we’ve been doing these video tips-of-the-week for SiX years now. We have completed or collected around 300 little tidbit introductions to various resources through this past year, 2013. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 II (next week).

Annual Review VI:

January 2013:
January 2: Annual Review V part deux
January 9: The New and Improved OMIM®
January 16: InSilico DB
January 23: ZooBank and species nomenclature
January 30: ScienceGameCenter #edtech

February 2013:
February 6: MotifLab workbench for TFBS analysis
February 13: UCSC Genome Browser restriction enzyme display
February 20: ENCODE Data at UCSC (reminder)
February 27: NetGestalt

March 2013:
March 6: NCBI Genomics Workbench
March 13: FlyBase
March 20: figshare + GenoCAD = outreach
March 27: Enzyme Portal and User-Centered Design

April 2013:
April 3: Phytozome and the Peach Genome
April 10: Introductory Cheminformatics
April 17: Sharing H7N9 data at GISAID.org with EpiFlu™
April 24: Cancer Atlas roadmap

May 2013:
May 1: My Cancer Genome
May 8: Transfac (and HGMD, Proteome, etc)
May 15: Influenza Research Database (IRD)
May 22: Canary Database for sentinels of human health
May 29: QIIME for Quantitative Insights Into Microbial Ecology

June 2013:
June 5: Prezi and other nonlinear presentation methods
June 12: TrioVis for family genome data sets
June 19: ENCODE ChIP-Seq Significance Tool
June 26: InnateDB, Systems Biology of the Innate Immune Response

Video Tip of the Week: Advanced Topics in GenoCAD

Recently we announced our newest training materials on GenoCAD. The introductory tutorial provides a great foundation for understanding the features that are available and how it could help you in the lab. But for those folks who want to take their design skills further–now you can use the GenoCAD Advanced Topics materials to do so.

As before, these materials are freely available for you to use because they were provided by the Peccoud Lab. There is a video that covers the same ground that you can find in the slides, but the slides are available too in case you’d rather cover the material with some workshop attendees or in a classroom. The exercises are there as well. Click on this image to go to the full video. It’s longer than our tips, of course, but worth it.

Click to access the tutorial suite with video, slides, exercises.

Click to access the tutorial suite with video, slides, exercises.

This relies on having completed the intro part, so don’t forget to accomplish the import that is needed from the first round. And if you want to see a bit more about the export of GenBank format files you might also want to see our quick tip on VectorEditor.

In this tutorial we examine the idea of creating custom grammars for a project that you might need to use–say, for example, chloroplast expression systems that are specific for your model system. We point you to the features you need to establish or modify to create a custom expression grammar for a system like that–and now conveniently we have a paper that describes that need and those aspects in more detail (linked below).

So check out the computer-assisted design features of GenoCAD and see if they can benefit your lab, or consider incorporating ideas from this material into classroom sessions. It’s a good way to get students thinking about important engineering concepts for synthetic biology.

Quick links:

GenoCAD Advanced Topics suite: http://openhelix.com/genocad2

GenoCAD site: http://www.genocad.org

Figshare required import file: http://figshare.com/articles/GenoCAD_Training_Set_I/153827

References:
Wilson ML., Hertzberg R., Adam L., & Peccoud J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD Methods Enzymol. DOI: 10.1016/B978-0-12-385120-8.00008-5

Wilson M.L., Okumoto S., Adam L. & Peccoud J. (2013). Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors, Bioinformatics, DOI:

Video Tip of the Week: VectorEditor

For this week’s video tip of the week, I’ll give you a quick tour of the VectorEditor software. It’s a handy tool that you can install locally, or use on the web, to edit and display features of your DNA constructs. It’s got all of the key features that you might want–annotations, graphics, sequence, restriction sites, 6-frame translation, and more.

Their succinct description:

Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.

But it’s so quick and easy to use that some people might find it really handy for introducing students to some of the concepts.

I came across it thanks to the GenoCAD team. They have sponsored us to create training materials, and one of the things we wanted to demonstrate was that you could take a DNA design from your computer-assisted design collection at GenoCAD, export it with GenBank features, and upload that into other tools that are compatible. Then the GenBank features become items in the new display or other tools you might use. They showed me VectorEditor as a sample of how easy that is.

So in this video tip I’ll show you how I take a design from my GenoCAD collection, load it into VectorEditor, and we’ll see some of the cool features they have in their software.

Quick links:

VectorEditor working demo web tool: https://public-registry.jbei.org/static/vesa/VectorEditor.html

VectorEditor software: http://code.google.com/p/vectoreditor/

GenoCAD web tools: http:www.genocad.org

GenoCAD tutorial suite (freely available because it is supported by NSF funding to the GenoCAD team): http://www.openhelix.com/genocad

References:

Ham T.S., Dmytriv Z., Plahar H., Chen J., Hillson N.J. & Keasling J.D. (2012). Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools, Nucleic Acids Research, 40 (18) e141-e141. DOI:

Wilson M.L., Hertzberg R., Adam L. & Peccoud J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD., Methods Enzymol., 498 173-188. DOI:

Hector Plahar and Joanna Chen are the team listed on the software page and gave me these additional details for the acknowledgement: Developed by researchers at the US D.O.E. Office of Science’s Joint BioEnergy Institute, at Lawrence Berkeley National Lab.

Video Tip of the Week: Mobile-device enabled tutorial suites

For decade now we’ve been offering our video tutorial suites to help people learn how to use bioinformatics resources. We’ve used a couple of delivery platforms, and we’ve changed the website a few times. But we also know that people like consistency with software, and if there are going to be major changes to the behavior of something, there better be a good reason.

We have a good reason. With the rise of mobile devices and the increasing use of them by students, our subscribers wanted us to make watching the tutorials on iPads and Androids and Surfaces more friendly. So we’re doing it.

This week’s video tip demonstrates the change to our tutorial movies that we’re rolling out. The basics are the same–each video offers details about how to use the software features at some database or tool site. We explain the display features, and the search mechanisms. We offer the video as well as the slides and some exercises to use as well. The only thing we’ve changed is the menu and controller options. The YouTube video here illustrates that.

So soon when you launch a tutorial video, you will have to swipe over the edges to access the menus and the slider. You can still click individual chapters, or move ahead with the controller. But those items move out of the way when you aren’t using them.

Everything else is the same. The landing pages for each tutorial suite will still have the launch buttons for all the items you need to access everything.

For subscribers, all of the suites will have this new functionality. If your site doesn’t have a subscription, you can still try it out on our sponsored training suites, such as: GenoCAD, OMIM, UCSC Genome Browser, or anything else from the “free” tutorials page: http://openhelix.com/free .

To learn more about our philosophy of training materials, you can check out our paper (below). Regular readers may already understand what we do, but if you are accessing these for the first time it might help you to know more about what we offer and how we do it.

Let us know if you have any issue with the new interface and we’ll take a look right away.

Quick link:

Free tutorials to try out: http://openhelix.com/free

Reference:

Williams J.M., Mangan M.E., Perreault-Micale C., Lathe S., Sirohi N. & Lathe W.C. (2010). OpenHelix: bioinformatics education outside of a different box, Briefings in Bioinformatics, 11 (6) 598-609. DOI:

GenoCAD training action shot

Recently we had a training at WashU on the GenoCAD tools that I mentioned before–the ones that are currently the “most viewed” item on figshare: computer-assisted design tools for synthetic biology. And the Peccoud lab has posted a brief report on that session on their blog, with photo of me doing the training:

GenoCAD tutorial at Washington University in St Louis

It was a great opportunity to workshop the new training materials (which you can access over there). We are now making a few tweaks to make the sessions even smoother, and we’ll have the recorded versions up soon.

There’s an opportunity to get this training coming up at the end of July at Tulane if you are there–contact the Peccoud lab for details on that one from their blog.

The GenoCAD site: http://www.genocad.org/

Edit: two opportunities for more GenoCAD training came across twitter yesterday with more details. Just wanted to add them here.

“Most viewed” item in figshare is….software training?

So if you go to visit figshare today, and you click the “Browse” link at the top, and then you select to sort by “most viewed” from the menu, what do you get?

figshare_mostviewed

Yes, for reasons I cannot explain, work that we’ve created or uploaded appears right at the top–the GenoCAD training we are developing, and a copy of the UCSC Genome Browser intro slides. Honestly–how we are beating “World Beer Consumption and Scientific Productivity” completely stumps me. I am rather pleased to see that the herring transcriptome is ranking so high too though.

I was joking on twitter the other night, though, that a #1 viewed rank and $3 will get me a cup of coffee at Dunkin’ Donuts. I’d love to see if this has any value in a grant situation, but I have no idea if it would. But it does make me wonder how and why this has happened. Is it really reflecting interest, or a need? Or is there some other way to interpret this?

Software training on genomics tools is a curious thing. A lot of people tell us how much they need this, and they appreciate the training which saves them lots of time in their work. We know we improve their awareness of what’s available, and their efficiency. At the last workshop we did at WashU, a woman in the back of the room emitted a huge sigh during Trey’s advanced UCSC section. Trey was worried that he’s confused her, but instead she said that in fact what he had just shown her saved her a ton of work. She was actually just incredibly relieved to learn what we could show her. And we see this a lot. But we have no way to measure that really.

But other times we find–say in grant situations–that software training isn’t scoring very high in the priority list. Yeah, it’s not novel and innovated enough I suppose. The people who need the training have no mechanism to push upwards really and express the need or quantify it. It’s kind of individual–you need what you need, when you need it. But it’s not an organized demand that we can point to in any way. Yet just a couple of weeks ago I attended a Software Carpentry training with 120 women who wanted better knowledge of software tools. Demand is there. I wish it was better recognized how important and useful it is.

I’m gonna go get a cup of coffee. And then make some more training. Go figure.

Citations:

GenoCAD Tutorials. Mary Mangan, Mandy Wilson, Laura Adam, Jean Peccoud. figshare.
http://dx.doi.org/10.6084/m9.figshare.153827 Retrieved 16:33, Jul 08, 2013 (GMT).

World beer consumption & scientific productivity.. Christopher Lortie. figshare.
http://dx.doi.org/10.6084/m9.figshare.664162 Retrieved 16:34, Jul 08, 2013 (GMT).
Introduction to the UCSC Genome Browser. Mary Mangan. figshare.
http://dx.doi.org/10.6084/m9.figshare.96258 Retrieved 16:42, Jul 08, 2013 (GMT).

Video Tip of the Week: figshare + GenoCAD = outreach

For this week’s video tip of the week, I’m going to highlight the services of figshare. Figshare is a terrific resource for storing data, posters, papers, slides, code, movies, and more. Nearly any sort of digital item that you may be creating as part of your research or research communications projects can be uploaded to figshare and delivered to the world. It’s permanent, citable, and people can download and comment about anything you provide.

I’ll highlight some of the basics of figshare, but you should learn more about them in a couple of ways. At their site you can see the summary of the features they offer, and you can also see the publication I have attached below that provides some of the history and conceptual framework for figshare.

As publication and outreach methods are changing, and researchers would like to get demonstrable credit for their output that may be outside of the traditional publication system, alternative metrics or altmetics are being developed to serve that. Figshare can let you assess how many people have seen your items, downloaded them, and eventually there will be a collections of links to the citations for them. It also makes it easier for people who use your stuff to credit you properly for them.

The specific example I’ll illustrate is the recent figshare files that Jean Peccoud and  his group created, and where we have provided the training slides, as a package of training materials for their software and site called GenoCAD. Eventually we’ll have a video and full training collection hosted on the OpenHelix site, but for now we wanted to get the slides out for people to look at. The training also requires folks to upload some data, so the data to use is provided. The exercises to complete the intro training are also posted there. Anyone can try them out, comment, and we can get feedback on them.

You’ll note on that page that we have updated the items more than once. But you’ll still have access to the older ones if you needed them. The page is permanent, and changes are traceable.

Using figshare as a mechanism for outreach, communication, and citation is so terrific for science communicators. Recently Stephen Turner initiated a plea to the bioinformatics and genomics communities to improve their behavior: Stop Hosting Data and Code on your Lab Website. People are expressing a lot of frustration when they can’t find the software some team has said they have used, the sample data, or the full data sets that they used for a publication or presentation.  We know postdocs move on, and that links break. But figshare can help solve that. Figshare is also handy for folks looking for the materials you provide or have described somewhere. And really–there’s just no excuse for not storing your data, code, and any other research related digital materials there. I’m looking at you Sasquatch genome team….

An introduction to the features of figshare can als be found in their video:

An introduction to figshare from figshare on Vimeo.

Do take a look at figshare, and start using it. It will benefit you, and the larger science community as well.

Quick links:

figshare: http://figshare.com/

Stephen Turner’s plea to bioinformatics folks: Stop Hosting Data and Code on your Lab Website (By the way, Stephen also stored that blog post at figshare, so it has a handy citation you’ll also see below!)

GenoCAD training materials example on figshare: http://dx.doi.org/10.6084/m9.figshare.153827

GenoCAD website: http://www.genocad.org/

Peccoud Lab example of using figshare’s API to host the items:  http://peccoud.vbi.vt.edu/genocad-training-set-i/

 

References:

Stop Hosting Data and Code on your Lab Website. Stephen Turner. figshare. http://dx.doi.org/10.6084/m9.figshare.105125 Retrieved 18:22, Mar 19, 2013 (GMT)

Singh, J. (2011). FigShare Journal of Pharmacology and Pharmacotherapeutics, 2 (2) DOI: 10.4103/0976-500X.81919

Cai, Y., Wilson, M., & Peccoud, J. (2010). GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs Nucleic Acids Research, 38 (8), 2637-2644 DOI: 10.1093/nar/gkq086