Content:
1 BioDivCloud invitation
If the admin or one of the group admins created an BioDivCloud user account for you you must have received an invitation via email (see image below). Click on the link in the email and follow the prompted instructions to create a password for your account. User accounts can only be created by group admins or system admins. If you want or need an account for someone, please contact screenforbio@gmail.com.
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Fig. 01, Left Invitation mail to the BioDivCloud. Click on “Set your password” to create a password for your account. |
Fig. 01, Right Dashboard after login to the BioDivCloud. |
2 BioDivCloud Web interface
After log-in you will find several icons in the upper left representing different features the BioDivCloud offers. If you want, you can use the BioDivCloud not only as storage but also as desktop to organize your own work and your collaborations. The first icon, the circle, represents the dashboard. The second, the folder icon, represents the folder system of the cloud storage. Depending on your account you might see and have access to different folders. If you are member of the BiodivTeam you will see a couple of group folders all starting with “1” followed by a two digit number and a title (“e.g. 1_03_projects”). Group folders can be seen by all group members and can only be created by group or system admins. You might not have full permission to read and write in every folder or your permissions might be restricted to certain levels to avoid messing up of the folder system by people creating various folders. In some folder you will find Readme.md files, which give you more information on what’s inside those folders. You can create your own Readme.md files in the folders your created to give others and yourself orientation on what is to find in the respective folders.
In the following we the first two group folders will be explained more in detail as they are relevant for most users.
2.1 Folder 1_01_manuscripts/
For every user there is a folder inside the group folder 1_01_manuscripts/ (e.g. “1_01_manuscripts/test_user”). The subfolders therein contain manuscripts of publications or thesis chapters of the respective first author. Users can create new folders inside their respective directory, but they should stick to the naming schema of the department as it is described in the {d6} R-package. Please give your project a unique and descriptive name following the schema “species_country_topic_name” (e.g. “pseudoryx_vn_rediscovery_testuser_a”). Please use underscores and the international Alpha-2 encoding for countries.
d6::new_project("pseudoryx_vn_rediscovery_testuser_a") in R.
These subfolders should contain all important information to the project and document the whole process until publication. The easiest was to create such a new subfolder inside your respective manuscripts folder is to run the R function d6::new_project(). This will create an R project with a standardized directory with all the scaffolding we use for all projects in our department (see image above). It will also add several files needed for documentation of your project. Of course you can add additional folders and files if needed. It is strongly recommended to use projects for your manuscripts as they make sharing and cooperation much easier, because they contain all relevant data and information and R handles file-paths as relative file-paths inside the project folder. How to use the d6::new_project() function see also section 5.
For your own work the subfolders can also contain co-authorships, these must not follow the d6 folder structure. All BioDivTeam members have read but not write or sharing permission on the folders. Only the first authors have full rights. However, first authors are free to share or grant permission to other users on subfolders or files as they will. If you want to cooperate with members of the BioDivTeam you can use the advanced permission area under the sharing section (image above, right side) to set permissions. Doing so will display the folder within the 1_01_manuscript/ folder structure for the cooperator, if the cooperator has at least read access to all superior folders. Simple shares will be placed outside the folder structure and with an increasing number of simple shares this can make the folder structure of the cooperator quite messy. So, if possible please use the advance sharing option in the online web interface.
2.2 Folder 1_02_people/
For every user there is a folder provided where it is suppose to organize its work (e.g. “1_02_people/test_user”). The subdirectories under /02_people/ are by default only visible to the respective user, i.e. the user “test user” can read and write in this folder but no one else. You can grant other users permissions or share your folders or files as you like (see also under advances permission in the online web interface). However, these folders are not private as such and meant for work related topics. They are not displayed to the cloud admin, but the cloud admin could regain control over the folders if necessary, thus these are not private directories. Real private folders or files (were not even cloud admin has access to) are any documents or any folders that you create outside the group folders (indicated by different icon). All data created by an account outside the group folders are deleted once the account that created them is deleted. Cloud admin has no access to this data in any way. However, we request you to have all work related issues inside your 1_02_people/user folder.
3 BioDivCloud on your local computer with the Nextcloud client
Nextcloud offers a client that allows to synchronize a local folder on your computer with an online cloud folder. It integrates with your local file manager and allows you synchronization of local folder with the cloud but also to create share links or sharing of data with other Nextcloud users same way as with Nextcloud web interface. You can check out the official Nextcloud Client manual for more details.
If you are using an IZW computer you will most likely have it already installed on your as the institute uses Nextcloud also for it’s own cloud, the “IZW-Wolke” (German for IZW-cloud). Otherwise you have to install the Nextcloud client first (see 3.1 Install Nextcloud client). In case you do not have admin rights on you computer and if it’s an IZW computer please contact the IT of the IZW to help you.
3.1 Open Nextcloud client
If you have the Nextcloud client already installed open it and open the main dialog (Fig. 04, Left) and click and “
Add account” to add your BioDivCloud account to your profile. Then go to point 3.3.
3.2 Install Nextcloud client
If you have install client first you must first download the Nextcloud desktop client for your operating system. The installation procedure is the same as for any software application: download the program and then double-click it to launch the installation, and then follow the installation wizard. After it is installed and configured the sync client will automatically keep itself updated. After installation it is recommended to reboot your computer to ensure the Explorer extension is correctly loaded. After reboot the Nextcloud client will automatically start and prompt a welcoming window on your screen (Fig.04, Middle) where you are asked to connect to your Nextcloud.
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Fig. 04, Left Main user dialog of the Nextcloud client. Click on the to add your BioDivCloud account to your profile.
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Fig. 04, Middle Menu of the Nextcloud desktop client after installation or after when adding an account from the main user dialog. Click “Log in to your Nextcloud”. | Fig. 04, Right Enter the URl of the BioDivCloud into the text field and click “Next”. |
3.3 Add BiodivTeam account to client
Click on Log in to your Nextcloud to connect to the BioDivCloud a new window will appear (Fig.04, Middle). Type the URL of the BioDivCloud https://nx22080.your-storageshare.de into the text field (Fig. 04, Right) and proceed. Now your web browser should open and prompt you to login into BioDivCloud. Enter your user name and password in your web browser and grant access. After you did that, go back to the client window. Click on “Nextcloud” on the right side (Fig. 05, Left) to chose where your Nextcloud folder should be stored in your local filesystem. An Explorer window will open displaying your local folder structure (Fig.05, Right). Create a folder at the desired place, name it BioDivCloud, chose the folder and click on select folder. Now this folder will be synchronized with your BioDivCloud. It is convenient to place your Nextcloud folder inside your private home directory of your computer (e.g. “C:/Users/test_user/BioDivCloud” in MS Windows), especially when also other users have access to the computer. Placing the folder outside your home directory (e.g. directly under “C:/BioDivCloud” or “D:/BioDivCloud”) make it accessible for every user that is allowed to log into the computer. However, the partition where the operating system is installed and where thus your home directory is, is sometimes limited in space. If you have to store a lot of data on you local drive and if your storage capacity in your home directory is to small you might move place the Nextcloud folder outside your home directory. Otherwise this is not recommended (although it is shown on Fig.05, Left).
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| Fig. 05, Left Installation wizard after you granted access to your BioDivCloud. Click on “Nextcloud” to define where your local Nextcloud Folder should be saved. | Fig. 05, Right Create a new folder somewhere inside your home directory to be synchronized with your cloud and name it BioDivCloud. |
4 Sharing data
Basically Nextcloud offers you the same options to share data with others like they are familiar from other clouds like Dropbox, GoogleDrive or OneDrive. You can grant other users only read or write permission, permissions to create or delete files and folder within a shared folder, or allow sharing items with third people. A shared folder will be added to the root of another users Nextcloud.
Or you can create links that you can use for sharing for people that do not use Nextcloud. The link will open a browser window, which will lead only to the linked folder or file. You can set an expiring date or password protection for these links and shares, or you can disable download or allow only upload of data.
4.1 Sharing from the online web interface
To share a file or folder in the online web interface you have to click on the sharing icon 
and a sidebar will appear with the sharing options (see Fig. 03 above). To create a link click on the add icon . To restrict the permissions of the link please click on the more icon 
and select from the options, e.g. set an expiring date.
To simply share a folder or file with another Nextcloud user you can type it’s name or e-mail into the open field. The user will receive an email that it was invited to a data share and if it accepts the share the folder or file will appear at the root of its Nextcloud scaffolding. If you want to share files or folders with people inside the team it is recommended to use the advanced permission area (Fig. 03) of the online web interface. Here you can grant if single users or groups permissions (e.g. read only, read & write, allow sharing with others etc.). As mentioned before, if you use the advanced permission area the shared folders will appear within the normal scaffolding of the other user if it has also at least reading access to all superior folders. If the cooperator has no read permission to the superior folders, the folder will not appear in the cooperators folder structure at all. Thus please think twice if it is not easier to share a superior folder before your share two subfolders.
4.2 Sharing local folders from your computer
Of course you can also initiate shares from a synchronized folder if you have the Nextcloud client installed. To do so right click on the respective file or folder in your explorer and chose “Nextcloud” and go on “Share options” (Fig. 06 Left). The new menu offers you the same options, you can type an email address into the search field to share a folder with another Nextcloud user or a Nextcloud group (e.g. “BioDivTeam”) or you can create links for sharing (Fig. 06 Right). The window will also show you with whom you shared the folder already and you can edit those sharing permission here by clicking the more icon on the right side.
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| Fig. 06, Left right click on the respective file or folder in your explorer and chose “Nextcloud” and go on “Share options”. | Fig. 06, Right Sharing from your local folder offers the same options like the web interface. |
5 Create manuscript folders with {d6} package, new_project()
The goal of the {d6} R-package is to simplify the project workflow within the department “Ecological Dynamics” at the Leibniz IZW by providing a standardized folder structure, templates for reports and utility functions. The easiest was to create a new folder inside your respective 1_01_manuscripts/ is therefore to run the R function d6::new_project() to create a new manuscript folder (there are different views within d6 on what a “project” is, thus don’t get confused). This will create a standardized directory with all the scaffolding we use for all projects in our department. It will also add several files needed for documentation of your project. It is strongly recommended to use projects for your manuscripts as they make sharing and cooperation much easier, because they contain all relevant data and information and R handles filepath as relative filepath inside the project folder. To start a new project open R, set your working directory to your respective manuscripts folder and run the following comand in R d6::new_project("species_country_topic_name") to create a manuscripts folder (e.g. “pseudoryx_vn_rediscovery_testuser_a”).