It is has been a while since the last update! A lot has happened since the inception of CWGAP: I became an official PhD of Human Computer Interaction, I moved to SF and joined a new company, and since I left ISU they wanted to shut down the servers I had CWGAP running on. I thought I may leave it running for the existing users, but no go - they cut them off.
So CWGAP moves to the cloud! Luckily I had a backup of some of the code, but had to re-engineer things to work in a Cloud environment. This beautiful SF morning I finally figured out the last pieces and pushed it live. Although I will start having to pay for compute times, so I may have to figure out a modest pay from users so I don't go too far out of pocket. I may create an LLC and maybe see if I can grow CWGAP, and maybe more bioinformatic tools for a UX-based viewpoint! I hope this would be an area of growth in the field, to make new and better tools for biologists. And hey, we could start something great in the process! And no better place in the world than San Francisco to do it. Feedback, and if you can help on this is welcome!
This SVG stuff is getting fun. Since everything is drawn inside the browser you can do some interesting things with CSS and JavaScripting on the fly. Extending the use of the initial SVG release, users of cWGAP can now not only zoom/pan with better control and can have additional layers of interaction. I added some mouseover hovering and clickable events/highlights so if you find some connections you wish to investigate, you can follow them better. I also added dynamic hyperlinking to PortEco so each gene name will fire up a new tab on your browser for in-depth viewing.
This all really follows Shneiderman’s Mantra: Overview First, Zoom and Filter, Then Details-on-Demand. (Even though Shneiderman totally hit me in the head with a frisbee at the last CHI Conference - I am pretty sure he was aiming for my noggin too).
I really think many biologists can get lost in the ACTGs. Which is really why I built cWGAP. So you can step back and see the connections come to life, after all, “even the best statisticians often set their calculations aside for a while and let their eyes take the lead.” (Stephen Few, 2009)
cWGAP is now a threaded application and server (that is threadsafe). And whipped up a small "failed run" page if Genbank files explode. Also got the email to instantaneous. Oh, and if you really like your comparison you can even tweet it (gets the word out for the tool, so more people can use it!) That is all. kthanksbye.
SVGs, or Scalable Vector Graphics are gaining a lot of popularity on the web. With the rise of crisp 4k and "Retina" displays, crisp graphics on the web are getting more important all the time. Compressed and grainy images are just not cutting the mustard. With cWGAP's use of Circos, it supports SVGs - so I decided to use this. If you run a comparison now, it will create the usual results page - but when the user clicks the PNG image graphic, it will pull you to a page allowing the user to manipulate (pan, zoom, interact) with the SVG via the browser only limited by your local graphics card. And you can toggle individual components of the visualization as well (turning off individual connections).
Soon I would like to implement an easy way to follow these connections. Let me know if you are interested in more interactions.. with SVGs, it is only limited by the imagination! (Sorry that is kinda corny)
IslandViewer is a nifty little web-based tool to find predicted GI and virulence in a submitted genome. This is especially interesting in our bacterial genomes to find possible islands of virulence. IV has their own visualization, but has similar coordinates to cWGAP. The basic functionality is being imported to cWGAP and overlays the output visualization to quickly view possible genomic islands and virulence islands. This prototype functionality is available for a select few users, and will be available later for public use. Let us know if this is something you would be interested in using (it will help hurry that goal).
Web technology is great. I wanted to have a reliable user base (no weird remote servers running scripts), so user logon was a necessary step. OmniAuth (OAuth) is a great way to quickly log in using another service (in this case Twitter or Google) without having to create yet another login and password on another site.
An improvement on iterative analysis and more stringent results.
On some of our internal genomes we have been evaluating, we have been noticing slight overlap on the annotation. Mainly, the start and stop codon may interfere slightly and cause cWGAP's program to report a gene that overlaps 1bp - which is most likely false (but hey, it is biology.) We implemented the overlap analysis to create more stringent results to prevent false positives from showing up, but, of course, this may cause real results to be filtered. This depends on a lot of what has been done to the genomes. Your mileage may vary.
Read more...We are just getting this website off the ground and having it being tested by users for feedback. cWGAP is on an ongoing project, and we would love your feedback too. This started as an internal project, but we saw the need for other to run simple and fast comparative genomics across many genomes. This is our effort to deliver this to the scientific community.
Currently we are diligently working on getting this accessible to others (login, UX/UI elements, connections, info architechture, [n]). Please stayed tuned for development, and let us know if there is anything that would help in your comparative genomics. We are hosting off of a small server for the proof of concept. If people are liking this, we hope to expand!
