Information submitted through the support site is private but is not hosted within your secure CDD Vault. Please do not include sensitive intellectual property in your support requests.

Quick Guide

Access

To access the CDD Vault go to 
https://www.collaborativedrug.com/
 and click the Login link at the upper right corner.  Or go directly to
https://app.collaborativedrug.com/

Enter your Username (should be your email) and Password when prompted.  Click Login. If you have trouble logging in, you can reset (see this article) your password via the Forgot Password link.

Web-browser requirements can be found in this article

To get more help

  • Cheat sheets, a.k.a. one-pagers for print-out can be found here
  • Here is an in-depth tutorial - see also the menu to the left.
  • If you are reading this document, then you've already discovered the Support Portal. You will find training guides and FAQ's here for all aspects of CDD Vault, including Vision and the ELN. Use this Knowledge Base (support.collaborativedrug.com) to search for relevant help topics. 
  • Send us an e-mail, if you can't find what you need in the documentation (don't be shy!). 
  • Reference cards, or Cheat-Sheets are found in the Downloads section.
  • Whenever you see and click the question-mark symbol "?" you can obtain context relevant help in a pop-up box.
  • Here's a detailed glossary of terms.
  • You can also find some short introductory videos on our CDD Academy Youtube Channel (click on the picture to open a new window).

youtube_stub_400x225.png

 

Overview and Getting started

  • The Explore Data tab is the first page you’ll see.
    • If you are a subscriber of CDD Vault, it provides quick access to searching, most recent protocol (biological) and molecule (chemical) data, as well as other shortcuts.
    • If you are a public access user, you will see links to create a new search.
  • A vault is a private and secure database, which may contain multiple projects. A CDD project, similar to a research project, is a collection of pertinent chemical and biological data, as well as a group of people sharing these data with each other. All data in your CDD vault must belong to at least one project.
  • You can selectively filter and search data on the Explore Data tab, by toggling projects in the sidebar. Additionally, CDD supports a variety of public data sets, which are listed below your private projects. By activating a public data set, you are able to compare your private results with publicly available data.
  • ELN tab brings you to the electronic notebook section.
  • Import Data tab is used to upload chemical and/or biological data from files, assuming you have sufficient privileges.
  • You must be a member of at least one project to import data. When you log into CDD for the first time, you are required to create a new project for yourself, or to contact your vault administrator to join an existing project.

Explore Data

Data can be browsed, filtered, and searched on the Explore Data tab.

Selecting your own Private Project Data:

  • Filter private data by toggling specific Projects in the sidebar. Only data from the selected projects will be displayed and searched.
  • Click hide next to the project name, to remove a particular project from the sidebar quick-list. The project is NOT deleted, and can be returned to the sidebar by clicking Show/hide projects.
  • To browse molecules or assay results in the selected project(s), click on the MoleculeProtocol, or Plates tab in the upper right portion of the work area.

Select Public Data:

  • Search a public data-set alongside private Project data by toggling a name in the alphabetical list of available public data-sets.
  • Manage the public data-set quick list in the sidebar, or read the data-set descriptions by clicking More link at the bottom of the list.

Search Selected Data:

Unless explicitly defined, all search terms on the page are linked by “AND” logic, i.e. all conditions/values must be satisfied for a “hit” to be returned.

  • Search by Protocol: (choose available protocol types and protocol names from drop down menus). You will be able to filter parameters by selecting a range of readouts.
    • Click Add a term link to add additional protocol search terms.  You can choose AND or OR logic between protocol terms.
  • Search by Structure: Click Launch the Structure Editor link to draw a structure, paste SMILES, or other formats.
    • Choose substructure or similarity searching by clicking the radio button next to either option; select a similarity percent value from the drop down menu.
  • Search by Chemical properties: enter the numerical values and ranges for the chemical properties listed. 
  • Search by Molecule keyword: choose “any field” or specifically select a search field from the drop down menu:
    • type the keyword value in the box below: you can use AND, OR, and NOT to create logical searches across these keywords.  (e.g. enter multiple molecule names with OR terms between names to retrieve a list of molecules) The molecule related fields listed in the drop down menu will be searched for the keyword value entered. 
    • Use " * " (asterisk) wildcard with any selected field. Wildcard search will return molecules that have any value in the selected field. If no field is selected, all molecules in the selected projects and public data-sets are returned.
  • Search by Collections: you can also narrow your searches by in/excluding collections existing within your projects.

Saved Searches:

  • Once you have created a search, save it for future use by clicking on the link below the search form, enter a descriptive name, then click Save at the lower left portion of the form.
  • Click the Saved Searches tab; and click Search next to the query name in the list of saved entries. 

Importing Data to the vault

Assay results and molecule data are added into specific projects. You will not see the option to manually add data or to import from file if:

  •  You do not have any projects in your Vault.
  •  You do not have the right level of access to edit or add data to the Vault or project.

Create a New Molecule (single compound, manual entry):

Detailed step-by-step tutorial

You can add new molecules manually by clicking the +Create a new... button on the Explore Data sidebar.

  • Click +Create a new... Molecule.
  • either: Type or paste in the SMILES string, MOLfile (or SDF string), or IUPAC, even most commercial names for known compounds in the Structure box.
  • or: If you prefer to draw a structure, click Launch the Structure Editor link to open ChemAxon’s MarvinJS.  Once complete, click Use this structure to paste the drawn structure into the new molecule record.
  • Select a project where this molecule will be assigned (required) and then click Create Molecule.
  • A new page opens when the structure is registered, where you can see the automatically generated molecule name (registry number), or edit the core definition and structure, add user-defined fields, create new batches of a molecule, and manage project access for this molecule.

Import a Compound Library from File

Detailed step-by-step tutorial

Bulk import of dozens or even tens of thousands of compounds is easily done by following the Import Data wizard through 3 simple steps.

  • To enter data in bulk, you can import from .sdf and .csv files on the Import Data tab (step 1). Here you also assign the project association. 
  • You can upload compound libraries from .sdf files with MOL structures, or from .csv files with either SMILES strings or IUPAC names (not both). F
  • On step 2 of the Import Data wizard, you will go through a “mapping” process, where you instruct the database how to match your file to the available database fields, and which columns to import.
  • The same mapping process is used to import assay (protocol) data.
  • The fields you choose for mapping will vary depending on the type of data, but will generally include a molecule identifier (molecule name), molecule structure, and/or assay results.
  • It is not mandatory to map every field in your file. If you wish to skip some data, leave the default Do not import  as your mapping option.
  • The last data import step is an import validation report that will inform you of all the events that occurred during your import. You will see lists of errors Suspicious, and Noteworthy events.
  • Review the Import Validation report carefully, and decide whether to Commit Data Import, or to Reject Data Import.

Create a New Protocol

A protocol record is a place to store results "non-chemical" data associated with a compound and batch, e.g. assay data. There will most likely be at least one CDD protocol for each laboratory assay. Here is the detailed step-by-step tutorial.

You can define new protocols  by clicking the +Create a new... button on the Explore Data sidebar.

  • Click +Create a new... protocol.
  • Give the protocol a unique name (required).
  • Enter the Category of protocol (required). This is a general grouping of your protocols that can be used to filter data on the search tab (e.g. SP, ADME, Cell, Enzyme)
  • Enter a brief Description of the methods or key parameters (optional).
  • Select the project where this protocol will be created (required). 
  • Click Create Protocol.  A new protocol page opens, where you continue to build the protocol by adding readout definitions. You can also modify the core definition, associate files, and manage project access on this page.
  • Create at least one readout definition in the new protocol (required). Readout definitions represent the types of assay results that you will store in this protocol, and you should create one readout definition for each result type (i.e. Raw Data, % Inhibition, Cell Line, Concentration, etc.).

Add a Run of a Protocol

A Run contains the set of data from an experiment done on a given day (step-by-step tutorial).

  • Runs belong to protocols. Add a new Run from the Run Data tab of the Protocol form (required for manual data entry). Alternately, create a new Run when you import from a data file (see next section).
  • To add data manually, one molecule at a time: select the specific Run date, click the Add a readout link, and fill in the form.
  • Biological results are linked to a molecular structure by the molecule name, so you will need to know the Molecule Name AND Batch Name for each biological readout entered.

Import Biological Assay Results from file

Importing data points (readout data) into your protocols and associated runs is done via our three step wizard, the same as is also used for bulk structure import (See above). [step-by-step tutorial]

  • You can import biological assay data into a CDD Protocol and Run. Follow the steps above to create a Protocol manually, then upload a data (.csv) file and follow the import wizard.
  • Biological results are linked to a molecular structure by the molecule name (molecule identifier). Make sure your file includes a molecule identifier for each piece of biological data. You can also use a unique plate name and well, assuming the plate has been registered in the CDD Vault.
  • You will have an option to select a specific Run of a Protocol that you have previously created, or to create a new Run.
  • On step 2 of the Import Data wizard, you will go through a “mapping” process, where you instruct the database how to match your file to the available database fields, and which columns to import.
  • The same mapping process is used to import compound libraries and biological assays.
  • The fields you choose for mapping will vary depending on the type of data, but will generally include a molecule identifier (molecule name), molecule structure, and/or assay results.
  • It is not mandatory to map every field in your file. If you wish to skip some data, leave the default Do not import  as your mapping option.
  • The last data import step is a quality control report that will inform you of all the events that occurred during your import. You will see lists of errors Suspicious, and Noteworthy events.
  • Review the Import Validation report carefully, and decide whether to Commit Data Import, or to Reject Data Import.

Collaboration and Data Access

Data can be private, shared, or public, but secure in all cases.

Private Data

  • The CDD platform allows for multiple levels of secure data sharing.
  • A CDD Vault is a private, secure database which contains at least one project.

Vault User Roles

  • Each user will have a unique username (= email address) and password and will be assigned a specific Vault role. Each Vault will have at least one Vault Admin (we recommend two administrators if possible).
  • Vault user-roles include Vault Admin, Full Access, Full Access-Biology, Read Add, Read Add – Biology, Read Export, Read Download, Read Only. Click on your user role in the top-right corner after logging into CDD to learn more.
  • Each user can create their own private project, or invite people from their vault to view project data on the Manage Projects tab.
  • Vault administrators will see every project in the Vault regardless of their membership on the Manage Projects tab. They can manage any project and add/edit memberships and users as needed.

Managing Data Access with Projects

venn.png A sub-set of data that is shared between projects A and B is accessible in real time to all users of both projects.

  • Data is shared by granting people access to a project within the Vault. The level of project access is based on Vault user-roles, with optional project specific permissions.
  • Data can be unique to a particular project, or shared across many projects. So a given project may have private and shared data, as shown in the Venn Diagram above.
  • When a project member updates a shared record, the modifications are visible to everyone with access to that record.
  • To share Protocol details, click Manage access to this protocol on the Protocol Details page (side panel). When a protocol definition is shared, none of the existing Run data is shared automatically.
  • To share a Molecule, click on Manage access to this molecule on the Molecule Details page (side panel).
  • Run data cannot be shared, but may be moved from one project to another. To move Run data to another project, click Move run to another project on the Run Details page (side panel). Once the data is moved, it will not be available in the original (moved from) project.

Public Data

  • CDD hosts an expanding collection of Public data that includes unique data-sets from big pharma research efforts, supplemental data from published literature, curated data from publications of interest, and research made public by select CDD users.
  • CDD will automatically notify you that public data is available for a structure in your private vault by displaying a link to a CDD Number on the Molecule Overview page (below the structure preview). You have the option to view the relevant public data next to your private results for the same structure. Your private structure and all associated data is always completely private.
  • Public data-sets can be selected for searching from the sidebar on the Explore Data tab.
  • Private data from a project or Vault can be made public, if and when you are ready to share, or once it has been published in a journal. Contact CDD (support@collaborativedrug.com) to learn how to make your results available to the research community.