Main Page

From iSee Wiki
Revision as of 11:08, 2 February 2011 by Root (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

What is iSee?

iSee is an intuitive and interactive approach for the dissemination of structural biology data. The SGC uses iSee to present methods, data and interpretation from its structural biology pipeline to a wide audience.

The concept has been developed by the SGC in collaboration with MolSoft LLC. All the features were implemented in the program ICM.

Where can I access more iSee datapacks?


Ways of accessing iSee

iSee is presently delivered in two modes: online, using the activeICM plugin, which enables an interactive window(s) in a web browser and standalone (offline) where information can be viewed and manipulated using a program installed in your machine, which doesn’t require internet connection.

This model is similar to that adopted by Adobe Reader – which also offers reading in both online (embedded into the browser) and offline modes ( through Adobe Reader installed in your computer).

The difference is in the fact that Molsoft LLC (the company that produced and distribute the programs) allows the user to install only one version (or both) as desired.

Installation instructions

ISee install 1mar10.png

Using an iSee datapack

Every iSee datapack has two main windows - one to the left with text and static images and one to the right which allows interaction with 3D objects. An expert mode is available in the standalone version and includes additional tools to extend the interactivity with the datapack.

ISee QRC 1mar10.png


Neat tips

  • Embedding datapacks as a component of MS Office applications - e.g. PowerPoint (Windows only)

You can embed an 3D interactive window of activeICM in any of your MS Office applications. This is very hendy if you are to give a presentation or a class using the contents of an iSee datapack. Imagine being a star on your next journal club by being able to show an interactive 3D image in a powerpoint slide!

Follow the instructions below, from the MolSoft website:

Embedding a datapack (.icb file) in PowerPoint 2003

Embedding a datapack (.icb file) in PowerPpint 2007

  • Extracting images

You can capture static images of any view you generate from reading the datapack. Simply use the screen capture function of your OS (or use a dedicated program for screen capture).

If you are using the standalone version (ICM-Browser), you can use the 'Quick Image' fucntion (File --> Quick Image) to extract only the representation seen in the 3D window to an image file. This will normally be saved either in your desktop or in 'My Documents' folder in Windows.

FAQ

Known Issues

  • Safari 4 browser and Mac OSX 10.6 ('Snow Leopard'): by default Safari 4 installed in machines running OSX 10.6 runs on 64-bit mode - this affects a wide range of applications and plugins.

Solution: configure the Safari 4 browser to run in 32-bit mode:

1.  If Safari is open quit Safari by going to Safari>Quit Safari
2.  Open a new Finder window and navigate to the Applications folder.
3.  In the Finder, select Safari.
4.  Go to File>Get Info.
5.  In the "Safari Info" window, open the "General" section.
6.  Select the check box "Open in 32-bit mode"
---
Safari 32-bit mode.png
---
7.  Close the "Safari Info" window.
8.  Re-launch Safari.

How to cite us

Three papers were published about iSee, exploring different aspects of the concept.

1. The fundamentals of the iSee concept:

Abagyan et al. Disseminating structural genomics data to the public: from a data dump to an animated story (2006). Trends Biochem Sci. 2006 Feb;31(2):76-8. Epub 2006 Jan 6.

2. The iSee concept applied to publishing:

Lee et al. SGC - Structural Biology and Human Health: A New Approach to Publishing Structural Biology Results (2009). PLoS ONE 4(10): e7675. doi:10.1371/journal.pone.0007675.

3. The underlying technology developed and used to publish iSee articles

Raush et al. A New Method for Publishing Three-Dimensional Content (2009). PLoS ONE 4(10): e7394. doi:10.1371/journal.pone.0007394.

iSee appearances elsewhere

  • Peter Binfield (editor of PLoS ONE) also demonstrated the iSee concept as implemented in the SGC PLoS ONE collection. This happened in 9.oct.09 at the UCSF. Have a look at the video of the talk. The bits about the iSee in the PLoS ONE starts after 19min40sec (you can drag the movie progress button to fast-forward). Listen to the 'ooos and aaaahs' from the audience :-).
  • Sean Connin on his blog Techne says: "It’s been several years since I experienced my first earthquake (...) I felt the same seismic tremor last week while working at the computer. This time it came with an online collection of digitally enhanced articles published by the Public Library of Science (PloS), under the title “Structural Biology and Human Health: Medically Relevant Proteins from the SGC”. "
  • Dave Bath on his blog Balneus reviews the PLoS ONE collection using iSee with an interesting title "Is it a bird? Is it a game? No… it’s SUPER JOURNAL!"
  • Jean-Claude Bradley have also mentioned us on his blog Useful Chemistry. He has also been heard saying that PLoS ONE's SGC collection is "history in the making" - see the video of his lecture on Scivee (@ 2min 34 sec).
  • The San Diego Union Tribune has published an article in their business section about MolSoft and the activeICM used in iSee datapacks. In the article 3-D software could give publishing a new angle Prof. Ruben Abagyan explains how the technology could be used in other fields.
  • The SGC/ PLoS ONE collection using iSee appeared in the 'Spotlight on Structural Genomics' section of The Structural Genomics Knowledgebase (PSI/ Nature Publishing Group).
  • Julie Thompson (Clustal alignment programs; IGMBC, Strasbourg, France) has mentioned the iSee concept as an example of how alignment visualisers in the future could be displayed/ implemented. The mention has happened during her talk at EMBO Workshop on Visualizing Biological Data (VizBi) in Heidelberg, 2010.
  • Charles Grisham, Professor of Chemistry at University of Virginia in Charlottesville, Virginia has been using ICM and ICM Browser Pro to 155 in his undergraduate biochemistry course. The students each took a different protein and, as part of their work for the course, created a "molecular document" for their protein (2010).

activeICM javascript detection code

This script detects if the activeICM plugin is installed in the user's computer.

The following instructions will help you to add this feature to the activeICM version of your datapacks and to give you an idea of how it works.

Please download the contents of the this folder before starting.


  • How to add the plugin detection functionality to an activeICM datapack

Let's say that you want to add the activeICM detection feature to the activeICM (HTML) version of one of your datapacks.

The folder where you generated your activeICM contains an html file called <datapack_file_name>.html

This html file is a set of two frames: a, b, referring to left.html and right.html files.

<datapack_file_name>.html looks like:

<html> 
  <head> </head> 
  <frameset cols="35%,65%"> 
      <frame src="left.html" name="a"> 
      <frame src="right.html" name="b"> 
  </frameset> 
</html>

right.html looks like this:

<html> 
   <body> 
       <OBJECT ID="ActiveIcmCtl" WIDTH="100%" HEIGHT="100%" type="application/x-molsoft-icb" data = "< my_datapack_file_name>.icb" />
       </OBJECT>
   </body>
</html> 


We need to change the contents of this file in order to add the plugin detection feature:

The new contents will look like this:

<html>
 <head>
  <title>
  </title>
  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  <script language="javascript" type="text/javascript" src="../communal/icbDetection.js"></script>
 </head>  
 <body>
   <script>
     composeICBdocument('my_datapack_file_name.icb');
   </script>
</html>

Please remember changing the src field to the location where you want to store the communal folder you have just downloaded.

So this is it! Once you transfer the folder with your bright new activeICM version of your datapack in an accessible place for your web server you have everything ready.


  • How the plugin detection script works


Let's walk through the javascript code.

composeICBdocument() function triggers the detection system. It first retrieves the local parameters the script needs to work: browser, OS, and the version of the activeICM plugin that the user has already installed if any.

Having done that, it connects to the SGC's web site to retrieve the latest available version of the activeICM plugin.

After a while the SGC's web server posts the latest version and only then the script re-writes the right.html file based on the user's browser situation.


function composeICBdocument(datapackFileName) { 
   getLocalParameters(function () {
       get_latest_version(function () {
           generateICBDocument(datapackFileName);
       });
   });
}


The javascript will only show the graphical side of the datapack if it is the latest activeICM plugin version installed in your computer. If not, it will re-write right.html with different messages.

The different situations are described in the fuction generateICBDocument().


If you want to modify the different messages just pick the function with the state you want to modify and edit the message var accordingly.


  • About XMLHttRequests

The question: How can I keep track of the latest available activeICM plugin version? is answered by using (asynchronous) XMLHttRequests.

The function get_latest_version(callback) will execute callback as soon as the SGC's web server has returned the value corresponding to this latest available activeICM plugin version

If the SGC's web server is behaving it will return the contents of an xml file where the latest versions for each (OS,browser,platform) are stored.

Then the function process_response(responseXML, callback) will parse this file to get the latest version.

Please keep in mind that this code will only work if and only if it is stored in a web server -accessible folder (and this server has access to the Internet). You can modify it to run locally removing the call to the function get_latest_version() and assigning the latestVersion variable with what you can see here