HomeWhy Challenges?All ChallengesCreate Your Own ChallengeContributorsForum
Sign in / Register

Grand Challenges Support

This page contains instructions on on how you can use www.grand-challenge.org to create your own project website. Be advised that this site is continuously developing. If you run in to any problems or have suggestions, please leave a message in the forum.

Contents

Create a project

  • Sign in or register as a new user - you will receive a validation email to activate your account.
  • Once you have been registered, create a new project by using the button on the Create your own project page.


     
  • Once created, your project appears in the project overview. Clicking your project in the overview takes you to your (empty) project page. You can admin your project with the admin link in the right upper corner of the site menu bar at the top of the page. You can also go to the admin page directly from here.

Add pages

  • Open the project admin page. Either click the 'admin' button on the left of the menu bar of your project, or go to the admin page directly.
  • Click the 'add new page' button on the bottom left. You can use the inbuilt HTML editor for basic editing. In addition there are several special tags available to render things like lists of files, and to insert html from external files. These are described further on in this guide.


     

Project data folder

Each project has its own data folder in which every file connected to this project is kept. Downloadable datasets, files uploaded by participants and results files are all kept here. You can also store all content of the pages of your project here, and use the instructions to include content from files. And you should store the images you want to use on the pages in your project in this data folder. You connect to this data folder using Dropbox. In the future, several syncing methods may be supported, currently only Dropbox can be used.

To connect to your projects data folder, do the following:

  • Sign up to Dropbox
  • Send us a message mentioning your project name and email address you used for your Dropbox account.
  • A share folder request will be sent to your Dropbox account, allowing you full control over your projects folder.

By default, files in the project data folder cannot be accessed by any url. There are two folders that form an exception to this:

  • /public_html  - Files in this folder can be downloaded and viewed by anyone, without logging in. This folder will contain for example images used on pages of your project.
  • /datasets - Files in this folder can be downloaded and viewed only by users that are logged in and registered to your project.

Making uploaded files available for download

To create a list of files which can be downloaded by users registered to your project, take the following steps.

  • Group all files you want to list into a single folder. We'll call this folder 'files1' in this example.
  • Put this folder inside /datasets in the project data folder. In this example you would end up with /datasets/files1.
  • Create a new page, set permission level to "Registered users only" and in the html of this page include the following tag: {% listdir path:datasets/files1 %}


  • When viewing the page, this tag will be translated into a list of file download links, one for each file in /datasets/files1 (see below)

Allow others to register for your project

  • Create a new page, and include the following tag in the page content: {% registration %} and save.


     
  • The rendered page will now include a registration link:


     
  • By default, registration is automatically approved for any user who is loggedin to comicframework, without notification to the admins. If you want to explicitly approve or reject any new participants you can turn on "Require participation review" in the "users" section of your projects' admin page:

    When this option is checked, the registration link  rendered by the {% registration %} tag will read "Request participation for...". When a user clicks this link, all administrators for your projects will receive an email notification of the new request. Participation requests can be reviewed using the "Approve or reject participation requests" link, also under the "users" section.

  • Upon acceptence or rejection the requesting user will be notified by email automatically.

Make your project appear in the projects overview

By default, new projects are hidden in the projects overview at grand-challenge.org/all_challenges/. To make your project appear in this overview

  • Go to the admin interface for your projects, open the "advanced options" section and uncheck the "Hidden" option.
  • Information on workshop date, associated conference etc. can be entered in the "Metadata" section of the admin interface.

Allow file uploads

Any logged in user can upload files to a project at the special /files page. The url for this page is fixed at projectname.comicframework.org/files. To make an upload page:

  • Create a new page, for example named 'submit'.
  • On this page include a link to the /files page. The best way to do this is to link to ../files by selecting some text, clicking the chain icon in the editor and putting '../files' as the url.

Including content from files on a page

  • To include text or html from a file in your project data folder, use the {% insert_file filename %}  tag.

  • Put a file in your project data folder, lets say we put 'results_table1.html' into folder /results for this example. The file could for example be written automatically by an evaluation script, and contain html to render a table.

  • Create a new page, include the following tag in the page content: {% insert_file results/results_table1.html %}  and save.
  • When viewing the page the content of results/results_table1.html will now be insterted in place of the tag.
  • Inserted file content can itself include other tags, like other {% insert_file %} tags, up to a maximum depth of 2.

Changing colors and other styling

You can customize the way your project pages using css (cascading style sheets). To use custom css on your project page take the following steps:

  • Place a file called "project.css" in the root of your project data folder. If you want to use a file with a different name instead you can set this in the projects Admin > Layout > Skin.
  • Edit project.css and add the css you want.

A full introduction on css is beyond the scope of this support page. A basic tutorial on css can be found here.

Allow others to edit the project

To allow other people to log in to the admin interface and also edit the pages of your project, take the following steps:

  • The other person needs to be Registered to grand-challenge.org. Get the username of the other person. This is the name in the upper right corner of each page when the person is logged in.
  • Go to the admin interface of your project (click the admin button in the upper right corner)
  • Open the 'Users' bar and click 'View, Add or Remove Administrators for this project'.
  • Users added in this dialog will be granted the same rights as you, including the right to add and remove admins.

Page permissions

For each page for three levels of access:
  • All - everyone can view this content in principle also non-logged in visitors.
  • Participants - Only people who have registered with the comic and have explicitly registered for your project are allowed to view this. Participants are not allowed to edit.
  • Admin - Only admins for your project can view this content. Admins for other projects can not. Currently, admins can only be added by the system administrators. In the future any admin can add new admins.

Adding images

To add an image use the following syntax: <img alt="" src="FULL_PATH_TO_IMAGE.png/" style="width: 800px; height: 312px;" /> as for example src="/site/mitos-atypia-14/serve/public_html/atypia_aperio_global.png/". To display precomputed plots from a template as done in LUNA16 when viewing FROC curves corresponding to a respective score on the Results page of that Challenge, use <img alt="" src="FULL_PATH_TO_RESULT_FROC_CURVE_{% url_parameter id %}.png/" style="width: 800px; height: 600px;" /> .

Adding a map with participants

Include the {% allusers_statistics %} tag to display the country of residence of all participants in the Comic framework . Include the {% project_statistics %} tag to display the country of residence of all participants in a respective Challenge.

Including an html table

Include the {% insert_graph results/.php type:anode09_table %} tag. Renders a csv file from the local dropbox to a graph.  This read in a file with the anode09 result format and outputs html for an anode09 table as shown after clicking on a single score value here. Anode09 results have the following format:
$frocy=array(0,0.00483092,0.00966184,0.0144928,0.0144928,0.0144928,0.0193237,0.0241546,0.0289855,0.02 etc...

Academic Torrents

How to share data with users using Academic Torrents

Academic Torrents is a distributed system for sharing enormous datasets - for researchers, by researchers. For a detailed description we suggest to visit the Academic Torrent website at this link. In order to be able to share your data-set within Academic Torrents you need to have a working torrent client. We suggest to use Bit Torrent. You can download BitTorrent from here.

How to create a torrent file

This procedure shows how to transform the data you want to share into torrent files:

  • Open BitTorrent.
  • Click on “New Torrent”.
  • Under the field “Select Source”, you can select the files you want to share into torrent. You can select a single file or a directory containing files.
  • Under the field “Trackers” put: http://academictorrents.com/announce.php (refer to Figure 1).
  • Click on Create and Save As to save and create your torrent.

Figure 1: Procedure to create a torrent from a file using BitTorrent

How to create a collection on Academic Torrent

The suggested way to upload torrents is to create before a collection of your data-set. A collection can then be filled with data-sets. Follow these steps to create a collection:

  • Go from your profile to “My collections”. In this page you can see the list of your collections.
  • Click on “New’” to add a new collection (refer to Figure 2).

In the next page you can create your collection providing a title and some additional description (refer to Figure 3).
 

Figure 2: Procedure to create a new collection in Academic Torrents

Figure 3: screenshot of the page for creating a new Collection

How to upload torrent files on Academic Torrents and add them to a collection

To upload new torrents please follow these steps:

  • Click on upload from the main page of Academic Torrents.
  • Under torrent file you can add your file.
  • Under the field type, Select Dataset.
  • Click on Upload to upload your torrent.

Figure 4: Procedure to upload a data-set torrent file

Logging into your page, clicking on My torrents you can see the list of uploaded torrents.

You can add the torrent to your collection, clicking on “ADD to collection and selecting the collection from a list (refer to Figure 5).

Figure 5: Procedure to add an uploaded torrent file to an exiting collection

Google Drive

Google drive is a service which offers the possibility of having free Google online storage. The available free space is only up to 15 Gb, so that if large data-sets are involved, Google drive is not advised. If a larger cloud storage plan is required, there is the possibility of purchasing it. In order to be able to use Google Drive a Google account is necessary. The first step is to upload files / directories on Google Drive cloud. The following step is to share these contents with users. Contents can be shared with users by providing them with the link to access shared files. This tutorial shows the procedure for uploading / sharing files. To add shared contents to your Challenge the usual "link" tool can be used while editing the respective Challenge page.

Dropbox

Dropbox is a file hosting service operated by Dropbox. Dropbox allows users to create a special folder on their computers, which Dropbox then synchronizes with. This allows the same folder (with the same contents) to appear irrespective of the device used to view it. Files placed in this folder are also accessible via the Dropbox website and mobile apps. The free version of Dropbox comes with an availble space of 2 GB. This means that the free version of Dropbox is not suitable for sharing larger data-sets. Furthermore,  the Dropbox service has a per day download limit of 250 GB, so that it is not advised as a means for sharing Challenge data. In fact, if a lot of users are downloading data during the same day, after reaching this limit, downloading is blocked for that day. The procedure to upload and share files with Dropbox is similar to the one used for Google Drive. To add shared contents to your Challenge the usual "link" tool can be used to edit respective Challenge pages.

All images appearing on grand-challenge.org are currently hosted on Dropbox.

Add Google discussion group

  • Go to https://groups.google.com/forum/#!creategroup and create your group.
  • In the Html box which appears on your new Comic project page (please see the Add pages section above) select 'Source'.
  • Insert the Google forum into your webpage by following the procedure given on the Google Groups help page and reproduced here below, replacing forum-name with your newly created Google group name.

<iframe id="forum_embed"
 src="javascript:void(0)"
 scrolling="no"
 frameborder="0"
 width="900"
 height="700">
</iframe>

<script type="text/javascript">
 document.getElementById("forum_embed").src =
  "https://groups.google.com/forum/embed/?place=forum/forum-name" +
  "&showsearch=true&showpopout=true&parenturl=" +
  encodeURIComponent(window.location.href);
</script>

Embedding YouTube video

The code for embedding YouTube videos may be found here and is given by:
http://www.youtube.com/embed/VideoID?autoplay=1
where VideoID is the alphanumeric string in the YouTube browser header following the '=' sign and autoplay=1 means that the video will begin to play automatically when it loads. Leaving out autoplay or setting autoplay=0 (default) means the video remains static until initialized.
With the autoplay option the '?' must be placed after the VideoID otherwise its presence is optional.

Embedding pdf file

To embed a pdf file use the following syntax: <embed height="375" src="FULL_PATH_TO_YOUR_PDF_FILE" type="application/pdf" width="1000"></embed> .
When embedding a pdf file from Dropbox, "?raw=1" needs to be appended at the end of the full path to your pdf file as: 
<embed height="375" src="FULL_PATH_TO_YOUR_PDF_FILE?raw=1" type="application/pdf" width="1000"></embed> . This string is required as it points directly to the file and not to the Dropbox default viewer.

 

 


Consortium for Open Medical Image Computing © 2012-