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  • NextBrowse: Web-based genomics visualization and BAM hosting tool.

    Hi everyone,

    This is my first post here. My name is Phillip and I'm a Masters student in computer science. I've been working on a new genomics visualization tool and BAM file hosting solution, NextBrowse, for the past few months. NextBrowse allows users to host BAM files and visualize both BAM and GFF Files. Visualization is done through CSS, HTML, and JavaScript. We currently require users to use the Google Chrom browser due to the specificity of the CSS, but we hope to extend it in the future to all browsers. I'd love to get everyones feedback here of what they like, don't like, etc.

    I've created a guest account for those that wish to try it out along with access to one BAM file for testing visualization.

    nextbrowse.vbi.vt.edu

    username: [email protected]
    password: guest123

    When logged in, simply click on the Browser link in the top right of the page and then click on the large Launch NextBrowse button.

    The top reference sequence of the browser is the reference sequence data of the currently viewed reference organism. The track area of the reference sequence displays where you are in the actual reference organism along with chromosomes.

    To add a track of data, move your mouse over to the right side of the screen and a side bar will expand for you to add a BAM file track.

    The track has 4 different levels of zoom, from nucleotide level of BAM reads up to the entire genome. When you zoom in, you zoom in too the current left side of the track. That is, if the track is currently at position YHet:1-5000 and you zoom in, you will be visualizing data from YHet:1-200. Tracks can also be searched individually or all at once. Tracks can add, remove, and search bookmark regions.

    NextBrowse also allows visualization and uploading of GFF files, but we aren't quite ready to release that aspect of the browser. Anyways, I look forward to hearing everyone's feedback and suggestions. Thanks!

    Best,

    -Phillip

  • #2
    The web server isn't working (TCP connection established but no HTTP response) from here - is it down at the moment?

    Comment


    • #3
      Hey arvid,

      Thanks for checking out the browser. I apologize for it being down, we're still working out the kinks. I just reset the server and everything should be back to normal. Please let me know if you have any other problems with it. Thanks!

      Comment


      • #4
        first impression : why chrome only? implementing common,open systems is good. don't tie yourself to google or microsoft or apple.

        second impression : very slow

        third impression : why annoying log in? doesn't even log in. just hangs "waiting".

        Looks like it needs a little more robustness.

        Where is this VPSed ? (i.e. where's it hosted?)
        What is it written in ?

        Comment


        • #5
          Originally posted by Richard Finney View Post
          first impression : why chrome only? implementing common,open systems is good. don't tie yourself to google or microsoft or apple.

          second impression : very slow

          third impression : why annoying log in? doesn't even log in. just hangs "waiting".

          Looks like it needs a little more robustness.

          Where is this VPSed ? (i.e. where's it hosted?)
          What is it written in ?
          Thanks for your response Richard. We are currently only allowing Chrome because the visualizations use a lot of CSS 3 and we decided to first gear it towards one platform to make development a bit easier. However, we are planning to add in the CSS and code for other browsers as well.

          Sorry about the slowness, we are currently working to resolve the speed issues.

          It's currently hosted on a dedicated server. The browser is written in Ruby on Rails for the backend and HTML, CSS, and JavaScript for the front end.

          Thanks and hopefully we'll have the speed issues resolved soon!

          Comment


          • #6
            Hey everyone, we are currently shutting down the server to figure out why it is running so slowly. Once we get it figured out, I'll post an update. Thanks!

            Comment


            • #7
              Originally posted by jack_bauer View Post
              Thanks for your response Richard. We are currently only allowing Chrome because the visualizations use a lot of CSS 3 and we decided to first gear it towards one platform to make development a bit easier. However, we are planning to add in the CSS and code for other browsers as well.
              I believe that very soon most browsers will support CCS 3 so this might become a moot point in the near future.

              Comment


              • #8
                it's still not responding ... "Waiting for nextbrowse.vbi.vt.edu" ...

                Comment


                • #9
                  I apologize for the server being down. I've tweaked a few settings and it should now be up and running smoothly now. Please let me know if you experience any more difficulties with accessing it. Thanks!

                  Edit: I'm sorry everyone, but the server is currently going down again. This is my first time deploying a server and it looks like the hardware that we decided to go with cannot handle the load. We are currently exploring other hosting options and I'll update everyone as soon as we get it online. Thanks everyone!
                  Last edited by jack_bauer; 01-31-2012, 01:01 PM. Reason: The server is currently down, so I wanted to update everyone.

                  Comment


                  • #10
                    Jack: Please do not get me wrong. I appreciate the effort that must have gone into this but before announcing something like this on a board like SeqAnswers.com you should have made sure that this was being hosted on beefy enough hardware.

                    Remember: You only have a short span to capture users with something like this. With a poor response from the server end not many will come back for a second visit.

                    And no .. I can't get the server to respond (just says waiting ..)
                    Last edited by GenoMax; 01-31-2012, 11:57 AM.

                    Comment


                    • #11
                      Hey Everyone,

                      I apologize for the server being down. I've updated a few libraries that I found out were known to cause memory leaks and from preliminary testing it seems that the server is now stable. So, please feel free to login to http://nextbrowse.vbi.vt.edu and let me know what you think. The guest account information is:

                      username: [email protected]
                      password: guest123

                      Thanks!

                      Comment


                      • #12
                        Ok, I can log in now, but apart from loading the example BAM and move the track around vertically I can't do much... While it does look fancy with all the colors, I don't even manage to browse around or zoom in and out, which I think are absolutely minimum requirements of a genome browser.

                        I don't mean to be rude, but in my opinion such basic features should be found within a few seconds glance of the user interface. I spent two minutes with it without figuring it out, and I'm used to figure out how to use badly designed user interfaces.

                        I agree with the post above, don't announce such an early version on a site like SEQanswers, you'll just irritate potential future users. There are enough functional browsers out there for me to avoid giving yours a third try.
                        Last edited by arvid; 02-02-2012, 05:49 AM.

                        Comment


                        • #13
                          Hi everyone, I want to apologize again for the technical difficulties. The site has been stable for over a week. If anyone is still willing to give me a chance I would be grateful if for no other reason that I need the feedback to complete this project and graduate. Any help/comments would be appreciated!

                          address: nextbrowse.vbi.vt.edu

                          The account details are again:

                          [email protected]
                          guest123

                          Thanks!

                          Comment


                          • #14
                            Any help/comments would be appreciated!
                            • Get it to work on firefox / iceweasel
                            • Make sure the screen after login looks different to the screen prior to login (e.g. change to the browser view, or a visualisation if possible)
                            • Don't show messages saying 'Log in to ...' if someone is already logged in
                            • Have an example GFF file already loaded
                            • Allow the browser window width to be increased / extended (i.e. not fixed width)


                            Those are all front-end changes. I've got no comment on the backend functions because it's not usable on my computer, except to make sure that it's an improvement on GBrowse and IGV (and preferably can support configuration files from those programs).

                            Comment


                            • #15
                              I'm not an expert in web development, but I believe the reason it only works for Chrome is because of the CSS3 support.

                              Comment

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