The Simpson Lab has adopted the Allan Lab template with add-ons from the OICR-WEBDEV team to facilitate high quality presentations and effective management of content and long-term communications.
Add-ons offer a variety of solutions to help your team get to the next level.
Here are a few of the most popular features that were used.
CMUI, a content management user interface to easily and quickly add markdown content and simplify the content publishing lifecycle. Best Practices bootstrap foundation for responsive site layouts to enable your pages to be viewed with mobile devices with different resolutions; semantic sharing and collaboration of research assets to enable your content to be shared (and searchable) with third-party services, including OICR-LABS.
Apps to manage collections of common pages found with Research Labs including Publications and Team pages. OICR-WEBDEV designs that can be found on our projects like cancercollaboratory.org and icgc.org.
Forms, integration with OICR-FORMS, to publish input workflows allowing your team to even integrate webhooks and streamline workflows with your favorite third-party services.
Github Login, a solution that is sustainable for researchers, allowing Github Pages to host your website, saving important resources typically spent on bandwidth and operations but also integrating Github login so your team enter your repository quickly.
Revision History and Forks, a complete history integrating with GitHub gives your team the ability to view prior changes, revert to previous versions, access revisions via the GitHub API, and even forks of full copies of your website for team collaborations and preparations for new website releases.
Friendly collaboration with the OICR-WEBDEV team for any support and customizations.
How to Get Started
All pages are written in markdown for easy editing, and Jekyll uses Liquid for the data-driven pages. The publication list, news items,and group members are stored as .yml data sheets (plain text) in the _ data folder, so that one can update the website easily. The pages are in the _pages folder. Updating and maintaining is easy using Github (not worldpress-easy, but there are other advantages (see e.g. this, or this). Jekyll takes all the markdown and data files, and creates beautiful html files in the _ site folder.
If you never used Jekyll, read the wikipedia article article and check out their website. Same for Github, which will host your first website draft.
Create and open a github account, go to our repository, and click 'fork'. This is now your copy of the website, and you can change and adapt it as you want. You don't have to link to us or mention us (but of course we appreciate it). Then change the name of the repository to "your_username" and the name of the branch to " gh-pages". Your website is now automatically published under your_username.github.io/your_username/. Except that it probably still looks like our website.
To modify the webpage, you can either do everything on on github.com (go to a file, click "edit", then "commit", "push"), or install Jekyll on your computer and play with your local copy that you sync with the branch on github.com. The former is much easier in the beginning, but a bit less convenient once you start rewriting everythint. To get it to work on your computer (and to learn a bit more about Jekyll), here and here are tutorials on how to use it and how set it up locally. Also, consider using the Github desktop app, I found it helpful.
Customise This Template
Now let's make this your website.
First, go to the news.ylm, publist.ylm, and team.ylm files in the _ data folder and insert your own data into the data fields. Watch out: Jekyll is quite strict about extra or missing spaces etc. Adhere to the format. In the beginning, test each change: commit, push, and check the published website.
For publications, you can add a "1" in the highlight field, then it will be featured prominently. You can add important news items (red, "newsl"), and less important news items (blue, "news2").
For the news items, just keep adding them. The first 10 will be displayed on the 'home' page.
For the team.ylm file
Next, change the content of all files in the _ pages folder. To change the title in the homepage, go to homelay.html in the _ layout folder.
Lastly, change the footer and perhaps header appropriately (in _ include).
You might also want to change the style or theme. I imported style files (in sass) from Bootstrap/Bootwatch, you can replace them with your own (in the _ sass directory). For small changes, just work on the override stuff in the main.sass file in the CSS folder. Or change some variables in the _variables.sass file, like the background color etc.
As said, Jekyll takes all the markdown and data files, and creates beautiful html files in the _ site folder.ln the end, either upload these files to your server, or buy yourself a domain and check the instructions on github on how to host it there.
Copyright and Credits
While this template is copyright free, we would welcome an acknowledgement if you are so inclined. Please notify us through email, so that we can add you to our growing list.
Working with Us
Join the OICR Labs community and work with OICR-WEBDEV to produce your lab site. Customise the template provided or opt for a complete redesign to create a site in alignment with your lab goals.
The Awadalla Lab was redesigned with a focus on good usability and aesthetics to establish a new team persona. The site used the modern technology stack provided by OICR-WEBDEV while saving resources of time, efforts, and expenses.
Visit us @ https://pawadallalab.org/