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1: Logging in and navigation

The CDD database was built for users who have no prior experience with scientific database navigation. In this lesson we will quickly go over key concepts of a vault and project and main application tabs, before diving into details in subsequent lessons. You will learn the initial steps of logging in and setting up your first CDD project- a required step before any other data can be added. 

Getting in

Setting up the first project

Explore Data tab

Import Data tab

 

Getting in

User Account

Your CDD account must be created by CDD support if you plan to import any of your private data into CDD. If this hasn't been done already, ask your own vault administrator to submit a request to CDD support, or you can always sign yourself up for a free read-only public access account. Once the account is created, you will receive an auto-generated e-mail from no-reply@collaborativedrug.com with your initial log-in information. If you do not find this e-mail in your inbox, it may have gone to spam, or was blocked by your mail server. The best way to avoid these problems is to simply add the no-reply@collaborativedrug.com address to your contacts list.

 

User Roles

Members are assigned a vault-wide user role, which will determine privileges across all projects. To learn what your role is, look in the top right corner of the blue CDD header: your role is shown right below your name. Click on the role to learn what privileges you have. This article describes all vault roles in detail. Typically, there will be one or two power-users with Vault Admin and Full Access roles, while the majority of members are either Read-Add, or Read-Export.

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The Vault

In addition to a user-account, you have a place to store your private database of structures and assay data. In CDD terms such a place is called a Vault. This is in analogy to a bank safe-deposit box: we create a private "box" for your data on CDD's secure servers, and grant access only to your group members. 

Just one user account is needed to access multiple vaults, however vaults are distinct databases with no automatic sharing of data. In addition to your main company vault, you may have a secondary "Sandbox" vault. This is a place to practice, test out new protocols or libraries, and evaluate CDD. All training exercises and practice runs should be done in the Sandbox! Here's how to switch between vaults: click on the vault name in the top left of the blue CDD header, and choose a name from the drop-down.

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Some vault settings can be configured by CDD support, and some can be configurable by your group’s Vault Admin. For example CDD support will configure the compound registration sequence in the vault, this is discussed further in Lesson 2.  A vault admin can customize terminology used throughout the vault if your group is not comfortable with CDDs default labels. For example, if you are working only with compound fragments, you can rename the "Molecule" record to "Fragment". If the term "Experiment" resonates with your group more than "Run", your vault admin can change that too.

 

Setting up the first project

What is a project

A CDD Project is a collection of related data shared with a particular group of people. Unlike distinct vaults, data in projects is related, and can easily be moved and shared between projects. CDD treats projects as a mechanism for keeping data private vs shared. All data within a vault belongs to at least one project, and unless you are a member of some project, you cannot view, browse or import any data at all!

For you, projects may represent the functional organization of all the members, such as different labs or organizations participating in the vault, perhaps medicinal chemistry in one project and high throughput screening in another. CDD projects may also represent scientific programs, such that when a single lab is researching three different areas. For instance, one might separate out cardiac, CNS, and oncology into different project.

When you log into CDD for the very first time, depending on your user-role, you will be taken directly to the Settings-> Vault->Projects page. If you are the vault administrator, you will see all projects and memberships, and will be able to add new vault members to the needed projects. For all other users, this page shows a subset of projects you have access to, and allows you to create a new private project. If you need access to an existing project, ask your vault administrator to add you.

TIP: As a vault admin, you are the only person that can see all members of the vault, and assign new users to existing projects. When adding a user to a project, you may choose to allow them to manage the project instead of you. This user will have ability to edit members, but will still not be able to add new vault members to a project. 

 

Creating a new project

Click the "Create a new project"  link in the top right corner of the Settings-> Vault->Projects page. Give it a name and a description that are representative of real projects you participate in, then click "Create Project". You can return to this tab later to add more members to your project, or to edit its' description. Now that the first required step is complete, you can start adding content to your new project, such as compounds and assay data.

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Explore Data

Picture 14.png Explore Data is the landing page once you log into your vault. You will use this tab for all searching and browsing, and shortcuts found in other parts of the application will always bring you here. The side-bar on the left shows all of the data collections available to you. The top section is a list of private projects, followed by publicly available data-sets.  Selections in the side-bar determine the context in which you browse and search, so make sure that relevant projects are selected. For example, if you are not finding a compound you imported last week, make sure that the necessary project is selected.
Notice the "Create New" button at the top of the side-bar. This is another place where you can create a new molecule, a new protocol, or even a project.
There are several tabs along the top of the main work space to the right. These tabs allow you to browse your data by "saved searches", "collections", molecules and protocols. All of these tabs rely on the data-context selected in the side-bar. For instance if you select one project, you will see only those saved searches and collections that belong to this project.

 

Import Data

The last remaining high-level tab is Import Data. As its name suggests, this is the place to import text-based data files, with a 3 step wizard to guide you along. Molecules and assay data may be manually created one at a time by typing directly into the page, but the most efficient way is to import in bulk: from a comma-delimited text file, or SDF file with molecular structures. Molecule data can be imported without any upfront set-up, and will be discussed in the following lesson. Biological assay results require some setting up before a file can be imported, and this will be covered in Lessons 2 and 3.

 

Summary

In this chapter we looked at all the main areas of the application. We learned how to log into your new vault, and how to set-up the first project. Now that this is done, you are ready to start importing data.

Next Lesson- Importing the first compound library

 

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