A Transcription Factor for GenomeBrowse: Using Evernote to enable sharing genomic analysis

         April 15, 2014

Science is a collaborative endeavor. Rarely is it in isolation that new discovery takes place. Unfortunately, using a computer to perform analysis is almost always a solitary activity. Sharing what you have found with members of your team often means squeezing around a small 13” glowing rectangle.

While looking at the same screen has its place, being able to save your findings and share them with a another person is enormously valuable. Even if the only person with whom you are sharing is yourself in 12 hours, decoupling time from analysis means that never again will someone be left wondering where that interesting variant was or what made it interesting in the first place.

We have wanted to integrate a way to “bookmark” into GenomeBrowse since it first launched. Many lunch-time conversations have centered around the best way to provide this functionality. Often GenomeBrowse is compared to a web browser. The idea of having a browser-like bookmark menu has a lot of appeal. But, unlike pages on the internet, a genomic region has no title, so seeing a list of Chr2:163,173,998 – 163,245,443, Chr4:53,499,919 – 54,278,649, etc does not help you remember why you bookmarked that region in the first place.

Ultimately the realization came that visualizing variants is reading a genetic story. And even if links to genomic regions are re-titled, 99% of that story is still not captured. What was needed was a way to provide context to each genomic region.

It was from the need to capture this contextual data that Gabe Rudy, and I began discussing the idea of integrating Evernote with GenomeBrowse.

Both of us are heavy users of Evernote in the office and in our personal lives. The ability to save almost anything you find into your own, searchable notebook is enormously powerful. After a while, it starts acting like an external hard drive for your brain. This hard-drive like flexibility means that there are endless ways Evernote can be used.

Evernote’s flexibility meant that it could act as the platform to provide the functionality we were wanting to add to GenomeBrowse to record the context of any variant so that someone else could easily understand what you found interesting. With that goal in mind, we build a two specific features into our note editor in GenomeBrowse.

Evernote integration in GenomeBrowse allows you to save screenshots, specific positions, links to areas of interest, and notes about your findings.

Evernote integration in GenomeBrowse allows you to save screenshots, specific positions, links to areas of interest, and notes about your findings.

First, we knew that coming back to the exact region in your view was extremely important. Using the bookmark button, a single click will capture the region as a link in your project. We didn’t want these links to just recenter the view on a location — capturing the view as you have set it up is crucial as, often, quite a bit of work goes into making sure that all features of interest are visible.

Second, images are vital to the storytelling process. We incorporated GenomeBrowse’s new “Save as Image” functionality to insert a screenshot at the click of a button. But, this screenshot isn’t just a “Print Screen” of your entire desktop. It is a high quality, publication-ready image of the plots that contain your findings. All of the user interface controls that might distract from your data is stripped away leaving just what matters.

Finally, other supporting data used during your analysis can be added to your note. Rows from GenomeBrowse’s feature table and annotation information from the data console can be copied into your note. You can also add links to any other source on the web. We believe these notes are a great way to organize your entire discovery process.

In addition to these features, rich text editing is available to annotate all your findings. Notes are automatically saved to the cloud and are immediately available through any of Evernote’s applications — web, desktop, phone, or tablet.

The real power of GenomeBrowse’s integration with Evernote is that easily enables sharing of your findings. The ability to share isn’t limited to other GenomeBrowse or Evernote users. From Evernote’s interface you can create a link to your note that you can share with anyone. If your collaborator doesn’t use Evernote, your link takes them to an web page with the note’s content. For those who do have GenomeBrowse installed, as long as they have access to your data files, they can pick up where you left off by opening the note in GenomeBrowse, clicking the genomic region links, and then add additional content to the note.

Evernote integration will be available with the release of GenomeBrowse 2.0 (still free!), currently scheduled for April 18th. Stay tuned.

We are really excited about the possibilities that this type of integration enables. Let us know how you use it! And we’ll be sure share our notes with you!

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