LaCava Research Wiki

1. Creating a tiddler

This can simply be done by clicking the ‘+’ in the menu on the right. Give your tiddler a title, e.g. description and date of experiment, and start typing your text. Automatically, only the source-code window opens, which is where you add your content. Since this is a source code, your tiddler will often look different than this. To show a preview of your tiddler, click the eyelash (outer right icon). You can just keep this preview open during editing.

You can add tags to any tiddler to cluster tiddlers based on e.g. project, experimental technique, or anything else. Use the ‘tag name’ field between the title and your main text for this.

If you would like to follow a template, a basic one for experimental entries can be found by searching for ‘entry template’ or clicking here. You can then click the edit-icon in the top-right corner, copy the source code, paste it into your own tiddler and go from there. You can then just discard the changes in the template and close it (top right corner, middle icon). Obviously, you can also let your own creativity flourish, possibilities are endless.

After you’re finished, make sure to save it (check sign in the top-right corner) and SAVE A LOCAL COPY on your own computer. This is to prevent any data loss in case the automated back-up system fails. Do this after you have saved your tiddler by clicking the down-facing arrow in the top-right corner > export tiddler.

2. Setting up server access for adding files

Since the full system runs on a server, any objects that you would like to attach to a tiddler, must also be placed there. This requires access to the server by means of an ssh key, and (s)ftp software. This server is also where all raw data will be stored. Accessing the server requires a RU network connection. At ERIBA, this thus means connecting through VPN.

First, create an ssh key and send it to Greg (ghouse@mail.rockefeller.edu), if needed with a request to VPN access. He will make sure you get VPN credentials and sftp access. Manuals to set up RU VPN once you have credentials can be found here. A windows guide to create a key is attached here. For Mac and Linux users you can run the following command:

ssh-keygen -b 2048 -t rsa -f ~/.ssh/id_rsa

Then please send ONLY the public key - ~/.ssh/id_rsa.pub. To send the key, just do "cat ~/.ssh/id_rsa.pub" and paste the output into an email. Greg will make sure your key travels the proper route to get access.

MAKE SURE TO WRITE DOWN YOUR LOGIN CREDENTIALS.

The second step is downloading sftp software. You can e.g. use https://cyberduck.io/ or https://filezilla-project.org/. Once the software is installed, and you are connected to the RU network, you can connect to the server:

Server: ruselfhost.rockefeller.edu
port: 22
username: rout_curator
password: your private key passphase
SSH private key: point it your private key file location on your computer

After you are connected, you can upload files to the following directories:

/WWW/sites/macromolecule-child.rockefeller.edu/tiddlywiki/scientific
/WWW/sites/macromolecule-child.rockefeller.edu/tiddlywiki/non-scientific
/WWW/sites/macromolecule-child.rockefeller.edu/tiddlywiki/Practice_Wikis

The easiest way is to create a folder for yourself in scientific/ where you will store all your future raw data. Please make sure to create small files to attach to tiddlers (.png), to maintain smooth running of the Wiki in the future.

3. Examples of added files

Once your files are copied to the server, you can attach them to any tiddler. This holds for true for any file, but only images and pdf files can be shown in the tiddler directly. Other files will need a link through which they can be downloaded. Make sure you have the preview screen open, so you can instantly see if the code correctly links to the image.

Image

Make sure the image size is decreased considerably compared to the raw file by creating a png file. You can now add the file by simply typing

[img["file_URL"]] 

in the source code box.

The URL starts with the folder after .../tiddlywiki/, e.g.

[img[scientific/Lars_raw_data/20200227_a-ORF2 IP/20200301_aORF2 IP/ORF1/ORF1merge.png]]. 

Spaces in the URL are not a problem.

PDF

Only add a PDF to the wiki if it is not too big and is of added value to the entry. Otherwise you can just add a download link as described below. Just as with the image, make sure it is on the server in the right folder. Use the following code:

<iframe width="100%" height="785" src="file_URL.pdf" frameborder="0" allowfullscreen></iframe>

Other files or external web links

Adding any other files requires creating a link by which people can download the file. This can be used for excel sheets or big PDF files or to link to external sites. Use:

[ext[text_you_want_to_contain_the_link|file_or_site_URL]]