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Craedl documentation

Welcome to Craedl, the Collaborative Research Administration Environment and Data Library. Craedl is a research data management service that understands the way academic research gets done.

Whether you are a student, principal investigator, administrator, or someone in between, Craedl works with you to help keep your work organized. Craedl enables you to share and discuss ongoing work with your collaborators, and to easily publish completed work for public consumption. Your research is easily accessible through Craedl's unified search utility, which enables you to use metadata to search your data, data that has been shared with you, and data that has been made public.

Craedl is in a beta testing state, and it is growing rapidly. Continue reading below to learn more about how to use Craedl. Should you find that you have any questions, concerns, or difficulties, please send an email to help@craedl.org.

Contents

Logging in
The basics
Sharing my data
Getting started with metadata
Searching for data (and everything else)
Discussing my work
Working in a research group
Working in an institute

Logging in

To log into Craedl, begin by clicking Log in in the upper right-hand corner. There are two different ways to log in: Using your institutional identity or using your email address directly. We strongly recommend using your institutional identity. If you do not yet have an account, continue reading to learn how to create one.

Log in with your institutional identity

First, try to log into Craedl using your institutional identity by clicking Log in using your institutional identity. This method of logging in uses the Globus portal to pass you to your institution and back to Craedl. Craedl requires that you log in with Globus in order to upload or download files larger than 150 MB because it uses Globus to accelerate the data transfer process.

Begin by looking up your institution in the Globus organization search bar. If you find it, click Continue to proceed to your institution and log in. If your institution does not appear in the search bar, you can select either Sign in with Google, Sign in with ORCiD iD, Use Globus ID to sign in, or go back to create a Craedl account directly with your email address. Note that Globus will prompt you to allow Craedl to access your Globus account and agree to its terms of service if you have not used Globus before.

After completing this process, you will find yourself back inside Craedl where we have logged you in and created an account for you if necessary.

Log in using your email address

Should you be entirely unable to log in with your institutional identity, click Log in using your email address on the Craedl log in page. Here, either enter your email address and password and select Log in with your email address or click Need to create an account? if you have never used Craedl before. After submitting the form, you will find yourself inside Craedl where we have created an account for you.

Logging out

To log out, hover over your name in the upper right-hand corner of the page and select Log out.

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The basics

Your personal Craedl

Upon logging into Craedl, you will be directed to the dashboard for your personal Craedl. From here, you can search the data that you have access to as well as other researchers, research groups, communities, and institutes.

You will see your personal data storage quota, which is limited to 100 MB by default during our beta testing phase. You can send an email to request@craedl.org to request additional storage space. You will also see your projects and your discussion notifications.

By hovering over your name in the upper right-hand corner, you will find your profile, a link to your Craedl, your active discussions, and any research groups or institutes to which your belong. Selecting a research group will take you to the Craedl belonging to that research group, which is distinctly separate from your personal Craedl, though it operates in much the same way. This is where you can collaborate with other members of your research group.

Data elements

Craedl has four different data elements designed to help you organize your work:

  1. A project, is the primary organizational element, and it is designed to contain a large research project, such as one that leads to a peer-reviewed journal article (smaller investigations are good candidates for projects, too);
  2. A directory, is an element of an organizational tree structure (like folders on your computer) that lives inside a project; you can create directories in the manner that best suits your workflow;
  3. An experiment, is an easily reproducible data element designed to organize repeatable workflows such as experiments, simulations, or analyses; and
  4. A file, is the data element that contains the actual data that you wish to store inside Craedl.

Each of these data elements can be easily shared with collaborators as described in the sharing section below. The permissions on a parent data element are inherited when children elements are created (for example, the collaborators in your project will automatically be added to any experiment that you create inside the project), but they can be modified at any time. With the exception of directories, data elements also assist in the definition and tagging of metadata as described in the metadata section below.

Projects

Projects are the primary organizational structure inside Craedl. Begin a new project by clicking Start a new project and give it a name. You can provide a longer-form about text, and you can link the work in this project to a community and/or a program should you like to. Communities are places where groups of researchers in a field agree upon a set of metadata common to that field of research to ensure everyone is speaking the same language. Programs are created by institutes to enable you to link the work you are doing to resources that the institute provides.

Upon creating your project, you will find that you are the only collaborator. Add more collaborators by clicking Edit and modifying the permissions as described in the sharing section below.

If you intend to use Craedl's automated metadata templating system to make your data easy to find later, now is the best time to spend a few minutes defining the basic metadata that you would like to record on files created in this project. If you linked your project with a community when you created it, you will already see some metadata provided in the project's metadata template at the bottom of your project. To set the default values for this community metadata, and to add specialized metadata for this project, click Edit metadata template.

Importantly, the selections that you make in this project's metadata template will automatically be assigned to any experiments or files that you create inside it, drastically simplifying the process for uploading files later. When adding additional metadata, consider the metadata section below.

Project data (directories)

To upload data directly to this project, click Project data, where you will be directed to the home directory in this project's directory tree. Here you can create a directory structure to fit your workflow and upload files to the project. These files automatically inherit the metadata that you specified in your project metadata template, but you are also given the opportunity to modify those metadata selections prior to uploading the files.

Experiments

If you commonly perform reproducible workflows, such as running experiments, simulations, or analyses, you can create experiment data elements, which inherit from their parent project and also provide another layer of metadata templating unique to each experiment. An experiment data directory tree lives inside each experiment so you can create a directory structure to fit your workflow and upload files to the experiment.

Files

Files live inside of directories and connect the raw data that you work with to the metadata that you have used to describe it. You can easily manage the sharing permissions on each file, which controls who can search for, view, and modify the file. A user must be logged in to view a file and to download the file's contents.

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Sharing my data

For the privacy of your research, you are by default the only user able to see your data elements. This not only includes forbidding direct access to others via URL, but also in search results: Users are only presented with results data elements to which they have access.

Craedl enables you to easily share any data element (project, experiment, directory, or file) with any Craedl user or with the public. You can share an entire project, a single file, or anything in between. Should you share a subset of the data elements in a project, any unshared elements will be completely hidden from the user with whom you shared the data elements.

To modify the permissions on a data element, click Edit on that element. You can edit the permissions on an existing user by clicking the pencil icon. There are three types of permissions that may be set for each user on any data element:

  • Read: The selected user may view the data element, but may not modify it;
  • Write: The selected user may both view and modify the data element; and
  • Admin: The selected user may modify the permissions on the element.

There are two ways to add new user permissions to a data element. Users with whom you have previously shared data elements will appear under Add a collaborator, and you should assign the desired permissions for this user before clicking Submit. You can invite new collaborators by entering your collaborator's name and email address. When you click Send invitation, Craedl will automatically assign the invited user read-only permission (you may modify this by clicking the pencil icon) and send an email to the address provided so they may connect your data element to their account.

You can easily make a data element publicly accessible by clicking Make public and revert that decision by clicking Make private. Permissions apply uniquely to each data element, so if you would like to automatically apply the permissions on one data element to all of the data elements it contains, click Apply permissions to all descendants. Note that this operation will overwrite any existing permissions set on those descendants. It may take a significant amount of time if the data element has many descendants.

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Getting started with metadata

Metadata describes the data that you generate and analyze in your research. It is invaluable in organizing, categorizing, documenting, searching, and discovering research data, but it can only fulfill these roles with the help of the researcher who generated the data (you!).

Craedl works with you to get the correct metadata attached to the correct files with as little human intervention as possible using its metadata templating system. Using the metadata templating system, you create the desired metadata fields and set the default metadata selections when you begin your project. Then, whenever you upload a new file, the file will automatically receive its metadata selections from the template and provide the opportunity to make any necessary modifications, saving you a significant amount of time for each file.

Once you have associated the metadata with your file, Craedl can immediately uncover your file through its search feature by querying terms found in your metadata. This can not only help you find your own misplaced data, but it can also help your colleagues find data relevant to their own research (as long as they have read permissions on your data to begin with). Should you wish to share your data publicly, this metadata will help other researchers around the world discover your work.

Further, by spending a few extra seconds ensuring the metadata on your file is accurate, you are implicitly building documentation for yourself and your colleagues. Future you (and the researcher tasked with extending your work from where you left off) will be grateful.

How do I know what metadata to use?

When adding metadata to a project, we like to ask ourselves the following question:

What information would a peer reviewer need to understand this data?

The better you can describe your data in your metadata, the easier it will be for others to find and interpret your work.

We encourage you to attach your projects to communities, which are designed to provide a minimum working set of metadata common to your field of research. If not directly applicable to your project, the metadata recommended by your community can help point you in the right direction when adding your own metadata to your project.

How do I manage my metadata template?

In your projects, you will see your community's metadata automatically appear in your metadata template. You may then add any metadata specific to your project. (And, if working in an experiment, you may add metadata specific to your experiment.)

To begin making changes to your metadata template, click Edit metadata template. To modify the default value(s) for each metadata already present, make your desired selections and click Save when you are finished. To add a new metadata field, click Add metadata. Craedl understands three different types of metadata:

  • Free input: The user can type anything they want into a text box;
  • Single choice: The user can select one option from many options; and
  • Multiple choice: The user can select many options from many options.

When creating a new metadata field, first give your field a descriptive label, which will be the name of your metadata field. Then, choose the metadata type and whether you would like Craedl to enforce that an entry be provided or a selection be made when a file is uploaded by checking the Required box. Note that, when editing the metadata template, if you provide a default metadata selection, the Required enforcement will always be satisfied. We recommend providing no default selection if you would like strict Required metadata enforcement.

Finally, add the values you wish to appear in this metadata field. For free input metadata fields, you may only provide one value, and it acts as the default input text. Leave the value blank to achieve an empty free input metadata field. For single and multiple choice metadata fields, you may provide as many values as you would like. Each value will represent one choice for that particular metadata field.

Save your new metadata field by clicking Save. When adding a new metadata field, you will be prompted to Add to future elements only or Add to all existing elements. This allows you to make modifications to your metadata template at any time in your project. By selecting Add to future elements only, Craedl will add the new metadata to your template without modifying other data elements that already exist in your project. Any new data elements that you add will inherit this new metadata as usual. By selecting Add to all existing elements, Craedl will add the new metadata to all other data elements that already exist in your project.

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Searching for data (and everything else)

Craedl's search functionality organizes multiple streams of information into two different levels. When you enter a search term and click Search, Craedl will show the top ten results in various different categories, including research data, groups, institutes, communities, and users. You then have the option to explore each category more deeply by clicking the title of the category.

Many of the categories search various different pieces of that category. For example, when searching for your name, you will be presented with the projects in which you participate. Additionally, when searching for data, Craedl will return not only file name matches, but also metadata matches in order to help you find the data you're looking for.

Searching in Craedl will only ever expose the data to which you have access. This means that you will not be able to search for data that belongs to someone else if you have not been given permission on that data (unless that data has been made public).

Search results with attached metadata are shown in expandable rows. Upon clicking on these rows, you will see different buttons representing each of the attached metadata. Clicking on these buttons will further specify your search by adding the selected metadata to the metadata label and value filters.

To limit your results, you can prepend a word with a minus sign (-) to exclude any results containing that word. This functionality is performed differently in verbatim mode (see below).

Filters

There are several filters that you can use to perform advanced searches and find your data more easily.

Verbatim: The verbatim filter is a very powerful tool that you can use to find exact matches on your data. You can use a single wildcard (*) at the beginning, middle, or end of your search term, which allows you to find data that begins and/or ends with the specified characters. Additionally, you can combine separate search terms with unions and/or intersections (denoted by || and &&, respectively) to filter the results further. You can also negate a search term (using !) to disclude certain results from appearing.

Name only: Only perform searches that match against the name/title of the desired results.

Metadata labels: Specify multiple, comma-separated metadata labels by which to filter results. You may specify whether you desire results based on the intersection ('And') or union ('Or') of these labels. The default is set to 'And'.

Metadata values: Specify multiple, comma-separated metadata values by which to filter results. You may specify whether you desire results based on the intersection ('And') or union ('Or') of these labels. The default is set to 'Or'.

Date of creation: Set either a starting date, ending date, or both to limit the creation date of the desired results.

Date of modification: Set either a starting date, ending date, or both to limit the modification date of the desired results.

Filetype: Specify multiple, comma-separated file extensions by which to filter files.

Include mine: Show projects, experiments, and files that are owned by you in the results. This filter is on by default when searching from My Craedl.

Include public: Show projects, experiments, and files that are accessible to the public in the results. This filter is off by default when searching from My Craedl.

Include research groups: Specify a subset of your research groups from which to include projects, experiments, and files in the results. This filter is off by default when searching from My Craedl.

Include institute groups: Specify a subset of your institute groups from which to include files in the results. This filter is off by default when searching from My Craedl, but on by default when searching from an institute.

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Discussing my work

When viewing data elements, research groups, institutes, and user profiles, observe the Discussion tab on the right edge of your window. Clicking this tab will expand Craedl's discussion feature, which provides a place for you to communicate with your colleagues about a particular file, experiment, project, etc.

You can follow a particular discussion to receive notifications when new messages arrive and tag a particular colleague using the @Colleague, Name syntax to request that Craedl send a notification. Only users who have access to the item to which the discussion is attached may view or comment on the discussion, and you may only these tag users. A bell icon (🕭) appears in the upper right-hand corner near your name when you have unread notifications, and you can view your notifications on your Craedl dashboards.

Discussions attached to user profiles are unique because they are public discussion forums where anyone may post a message to you that is visible to the public.

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Working in a research group

Craedl's research groups provide a convenient environment for collaboration in an academic setting. Research groups, accessible through a unique subdomain such as our development team's Craedl at craedl.craedl.org, may be customized by modifying the color scheme and basic about information. There are four roles that a user may take on in a research group:

  • Guest: limited read-only access to the research group;
  • Researcher: a research user such as a graduate student or postdoctoral scholar;
  • Principal Investigator: a research group leader with additional group management functionality; and
  • Administrator: a user with the ability to modify the research group membership.

Principal investigators and administrators may invite new users to the research group by clicking Edit on the research group's dashboard and sending an invitation. An invited user will be automatically assigned the Guest role, and roles may be modified by clicking the pencil icon.

Only principal investigators may create new projects and assign researchers to the projects, but once created, researchers with write permissions on the project have precisely the same capabilities as described in the basics section above.

If you would like to create a research group, send an email to request@craedl.org for more information.

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Working in an institute

Craedl's institutes provide advanced functionality to large groups of researchers working in a highly collaborative environment. In addition to various administrative tools, Craedl's institutes enable research groups to work together on broader programs of research. Institutional administrators may organize the resources that they allocate to their principal investigators into programs of research, which in turn may be grouped according to research topic, focus, or other definition. Programs of research act as a bridge between the institute and its researchers, who do their work within their research group Craedls, by linking the administrative information contained in a project.

Institutions may provide specially curated data to their researchers by attaching it to their organizational groups. These curated data sets are automatically shared with members of each organizational group as determined by their assigned programs of research, ensuring that users can see curated data only as needed.

If you would like to learn more about using Craedl to manage your institute, send an email to request@craedl.org for more information.

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