Tag Archives: video

VideoTip of the Week: ENCODE @ Ensembl

We have a lot of tutorials (2 in fact, ENCODE Foundations & ENCODE @ UCSC), tips and information about ENCODE. We also have a lot of tutorials (again 2, Ensembl and Ensembl Legacy- on the older versions ), tips and information about Ensembl, the database and browser at EBI.

Now here is a tip of the week on both Ensembl AND ENCODE. This is one of the more recent additions to Ensembl’s video tutorials. This video looks at how to identify sequences that may be involved in gene regulation. Most of this data at Ensembl is based on ENCODE data. This is using the “Matrix,” a way to select the regulation data you need based on cell types and TF’s. At the end of the 8 minute video they discuss a bit more about how to get all ENCODE data.

So, now you have a wealth of information here at OpenHelix through our tutorials and our blog about ENCODE and Ensembl.

Quick links:

ENCODE: http://encodeproject.org/ENCODE/
ENCODE @ UCSC: http://genome.ucsc.edu/ENCODE/
Ensembl: http://www.ensembl.org
ENCODE Tutorials: http://openhelix.com/encode
Ensembl Tutorials: http://openhelix.com/cgi/tutorialInfo.cgi?id=95

Video Tip of the Week: the New PubMed Filters Sidebar

In today’s tip I am linking to a YouTube video from NCBI that briefly explains the new Filters Sidebar feature that has been added to PubMed. We first saw a tweet that the change was coming back on May 2nd, just as I was completing a total update to our full PubMed tutorial*.

I struggled with whether to hold our production team for the new sidebar, or to produce our tutorial with the plan to update in the near future – it is always a struggle to know which is the best option because resource changes can occur at the speed of light, or according to geological time scales (ok, that’s an exaggeration but it feels that way when you want to release a wonderful, up-to-date project & something holds you up and causes delayed publication of our tutorial materials). With PubMed I was lucky – I saw a tweet that the sidebar feature would be added “in the next week”. I asked our voice professional to put the script on hold & I paced around PubMed waiting to see what (& when) things would occur.

True to their word, the sidebar feature showed up on PubMed results on May 10th, exactly one week since I had seen the “in the next week” announcement – my THANKS to the NCBI & PubMed Teams! :) Not only did they push out their updates in a timely manner, they made a YouTube video explaining the changes & discussing where future changes are slated to go. The video is clear, and quick, so I am using it as my tip this week. I’m not sure the feature is 100% stable, as I show in the image below, and describe later in the post, but I think the change might accomplish NCBI’s goal – for more people to notice & utilize filters for their searches.

In the video the narrator states that the filters area is gone & the two default filters are permanently selected, as indicated by the check marks that can’t be “unclicked”. I”m not seeing those check marks on either “Free full text available” link (shown) or the “Review” link, which is not in view in my image. I also see a difference as to whether I get the right filtered subsets depending on whether I am logged into My NCBI (the upper window shown in the back of the image), or not (the lower, front window). In my hands IE 9.0 & Firefox 12.0 both function similarly in these aspects.

The NCBI video doesn’t really show how results look after filters are added, but in playing with it to me it looks like all of your filters are applied to your search & you only get one set of results, not links to various subsets. Although it is now easier to add filters to searches, if that’s how filters are going to work going forward, I think I will miss the old filters – I kind of like being able to switch between various subcategories of results without having to change my filters or rerun searches. Be sure to share your thoughts & preferences with NCBI so that they can create the best resource for their users needs!

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick links:

OpenHelix Introductory Tutorial on using PubMed (soon to be updated): http://www.openhelix.com/cgi/tutorialInfo.cgi?id=70

PubMed Resource: http://www.pubmed.gov/

PubMed Reference:
Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S. & (2011). Database resources of the National Center for Biotechnology Information, Nucleic Acids Research, 40 (D1) D25. DOI: 10.1093/nar/gkr1184

Video Tip of the Week – The Cell: An Image Library

Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. The Cell Image Library is brought to you by the The American Society for Cell Biology (ASCB), and contains thousands of images, time series and groups of images, videos and animations of cells in a variety of organisms. Images are organized by Cell Process, Cell Component, Cell Type, Organism and Recently added. You can browse images or do a basic search from the homepage, or perform advanced searches. The advanced search form allows users to query with keywords, and for image attributes, specific image licensing categories, biological categories, imaging techniques, or associated anatomy terms.

To quote from their About page, the Cell Image Library:

“This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health.”

And the library doesn’t merely allow you to access images, you can also provide your own images to be featured in the Library, as described in their “contribute” page. You contribute your raw data or minimally processed data images or videos to them and they will  be annotated by professionals with broad disciplinary expertise. Each image receives a CIL, or Cell Image Library accession number, which can be used to reference an image.

In this tip I’ll touch on the features of the image displays, and anything else that I can fit in, but I can guarantee there is more for you to explore on your own. After watching our video tip, I suggest you head over to The Cell: an Image Library & check it out yourself. If you do, be sure to share your insights with the Library’s development team by filling out their user survey. Thanks!

Quick Links:

The Cell: an Image Library  – http://cellimagelibrary.org/


(On the utility of the Cell Image Library for science education) – Miller, K. (2010). Finding the key – cell biology and science education Trends in Cell Biology, 20 (12), 691-694 DOI: 10.1016/j.tcb.2010.08.008


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…

  • Nice video on RNA interference by Nature Reviews Genetics. You can access all of the featured RNAi multimedia links from this page, or go straight to the video on this page. [Jennifer]
  • Interesting, The Repertoire 10K (R10K) Project: RT @deannachurch: CG: go to http://t.co/rekf2Gkd for more information on joining the project! #AGBT [Mary]
  • And it’s not in the papers anymore… RT @genome_gov: Pachter: “My worst nightmare: the curse of deep sequencing” aka too much data. #AGBT [Mary]
  • Read a Nature Outlook on allergies from Nov. 2011 – lot of new philosophies & theories that I wasn’t aware of. Currently free full access is available to the Nature Allergy Outlook [Jennifer]
  • RT @andrewsu: Word cloud of NAR 2012 Database issue abstracts via http://t.co/TMtefZ0k http://t.co/2zRzZkEG [Mary]
  • Cool new option for PDB submissions: Volunteer Structures For Foldit [Jennifer]
  • RT @LouWoodley NYC tweeps – the next Science Online NYC is on March 20th on keeping the research record straight http://bit.ly/xwziUb #sonyc [Jennifer]
  • RT @GeneSherpas: “@GeneticsUpdate: Can You Be Fired for Your Genes?  http://t.co/fDaOriU” Hopefully our future doesn’t come down to this!” [Mary]
  • Ha! That was unexpected… RT @edyong209: Bizarre SNP study on genetics of choral singing. Abstract takes surprising turn in final lines. http://t.co/VkSU4fd0 [Mary]
  • RT @jacksonlab: Facing a rare #genetic disease together, the Wentzell family doesn’t let anything slow them down. #raredisease http://t.co/bscdUXoN [Mary]

Tip of the Week: SciVee, the YouTube of science

Every week we do a video tip of the week. Every week we use SciVee to upload and share that video (our account here). We now have nearly 50 tips and videos residing at SciVee. SciVee has been called the YouTube of science. Like YouTube, it allows you to upload videos, though in this case exclusively related to science. Additionally though, SciVee allows you to do some ‘science-specific’ actions you wouldn’t be able to do with YouTube or Vimeo. PubCasts and PosterCasts are two of several such features (Papercasts are similar to Pubcasts, only non-published papers). These features allow you to upload a video describing your research and then upload a paper and poster and sync the paper or poster to the video. This allows the author to describe the paper (or poster) and the research while the viewer can see the relevant sections of the paper or poster. There is more about how to do this here. A virtual poster session, or a virtual talk. Once you do that, you can embed your video on another web site (as we do here!) to share and allow others to share. It’s an excellent tool to share your research and get it to a wider audience.

Today’s tip of the week is a short intro to SciVee and a quick tutorial on uploading your own videos.

At the end you’ll see we have a community at SciVee called “Genomics Resource Training.” There you will see all the tips of the week we’ve done. In addition, we add other genomics and biological data resource tools and databases to the community when we find them. Check out and join the community:

Visit Genomics Resource Training Community

Friday Night & Nothing is On TV? Maybe Turn to TED

TED_logoTED stands for Technology, Entertainment, Design and their site offers you the opportunity to view talks on all sorts subjects given by all sorts of people with all sorts of points of view. I caught wind of TED from a BioTechniques post by Kevin Ahern – thanks Kevin! Of course for this blog I focused my attention on the biology talks – there are a bunch that look interesting to me – but the talks cover a wide range of subjects, as you can see from their talks tags list.  To quote TED on TED:

TED is a small nonprofit devoted to Ideas Worth Spreading. It started out (in 1984) as a conference bringing together people from three worlds: Technology, Entertainment, Design. Since then its scope has become ever broader. Along with the annual TED Conference in Long Beach, California, and the TEDGlobal conference in Oxford UK, TED includes the award-winning TEDTalks video site, the Open Translation Program, the new TEDx community program, this year’s TEDIndia Conference and the annual TED Prize.

So, the next time you think (or hear) ‘there’s nothing good on TV’, you might consider turning to TED – an interesting friend indeed.