BioMicro:Instructions

Instructions on how to use NExtSEEK

How do I upload data? What is an assay sheet?

When uploading to NextSEEK, it is required that samples are loaded through an "Assay Sheet." The system's functionality reads through these Assay Sheets and correctly distributes metadata to desired database fields.

Metadata sheets can be uploaded through the ‘Assay Sheet Uploading’ tab on the MIT FairData website. Choose a file from your computer to upload and click the green ‘Upload Samples” button. The upload may take a moment to process. When the samples have been uploaded, a Feedback Sheet will be provided.

Feedback Sheets

The feedback Sheet shows all the data from the Samples sheet that was uploaded and outlines any errors that may have occurred during the upload. Other attributes of feedback sheets include

• Providing the user with UIDs for every sample filled out.
• A message that pops-up stating the number of samples that were uploaded on the site.
• If not all the samples were uploaded successfully, the red highlighted series on the sheet can be used to determine which samples failed.
• The highlighted cells will contain information as to what could be the cause of the failed upload.

How do I upload a data or protocol file?

NextSEEK also collects records of data files that would be shared or deposited to public data repositories, such as DNA sequence FASTA files, RNA expression count tables, flow cell counts, and images

Protocols should be uploaded through the Data & Protocol File Uploading tab under Data Entry on the FairData website.

There is a file size limit of 1GB, however instructions for uploading a file of larger size are included on the upload page if necessary. In the upload tab drag and drop or click to upload the Protocol file.

Data uploads are accepted only if a matching sample record is found in the database. Any sample sheets should be uploaded prior to attempting to upload corresponding data. There is a 2GB limit on file size for Data and Protocol upload. Any larger files will need to be uploaded with our help.

How do I search for my samples?

Searching for samples and data can be done by navigating to the Sample Search tab under Data Query on the FairData website

• Use the Sample Type drop down menu to choose the desired Sample Type or Data Type for searching.
• To search just based on this type, click the search button.
• To further narrow the search, choose an attribute to filter by.
  • Use the Sample Attribute drop down menu and click one of the attributes to filter by.
  • Select the Operator drop down menu
  • Select ‘Contain’
  • Type the value of the attribute you wish to search for in the ‘From:’ string value box and click search. For example, to search for a mouse sample with the UID attribute containing the letters MAC, select ‘MUS’ in the ‘Sample Type’ menu, ’UID’ in the ‘Sample Attribute’ menu, ‘Contain’ in the ‘Operator’ menu, and type MAC in the ‘From:’ text box.
• If attempting to search for all samples or data that are NOT of some attribute, then choose ‘Not Contain’ in the ‘Operator’ box rather than ‘Contain’.
• The results of the search will be displayed as a list that can be downloaded, deleted, published, interacted with etc.

To download a specific sample(s)

• Click the blank square on the left side of the sample in the list.
• The square should then appear checked.
• Click the ‘Download samples’ button at the top of the list of samples, and an excel file containing the sample’s information should be produced.

To download all samples that have been searched for,

• Select the blank square just below the ‘Download samples button’.
• All the squares next to samples should appear checked.
• Click the ‘Download samples’ button at the top of the list of samples, and an excel file containing information about all of the samples should be produced.

Searching for Protocols

• Toggle to the data query tab in the menu bar on the fairdata website.
• A dropdown menu will appear with options for different searches or queries: choose “Protocol query”.
• To search for a specific ID, type the ID into the text box below the header “ID” and results containing that ID will appear.
• To search for a specific name or word(s) within a name, type the desired name or word(s) in the text box below the “UID” header.
• And so on, the same concept applies for all following text boxes and their corresponding headers.
• Once filtered by the attributes desired, a specific sample(s) can be downloaded:
  • Clicking the check box on the left-hand side of all the attributes and then click “batch download files selected”.
  • The user can also download all the samples by checking the top check box situated next to the headers, and then click “download file list”.

How do I access a sample/protocol/data file?

• To access any desired sample simply click on the blue UID listed, and the sample page will be opened in another tab.
• For protocols and data files, click the File URL to access the page.
• For samples, the page contains information about the sample and shows a Sample tree which demonstrates the relationships between this sample and other samples.
• To explore the other samples in a tree:
  • Click on the desired parent or child sample node in the figure presented on the webpage.
  • This opens the desired sample page in another tab that can be similarly interacted with.
• For protocols, a file will open that contains the desired protocol once clicked on.
• For data files, access is needed to successfully open them in certain scenarios, but a file will be available for download otherwise.

How do I delete a sample?

To delete a single sample, protocol, or data file, or all samples, protocols, or data files, follow the same selection instructions as described above for downloading, however instead of clicking the Download button, click the ‘Delete samples’ button. A message will pop-up requiring an addition step in order to confirm that the sample is being purposely deleted.

How do I write a data management plan?

The purpose of a data management plan is to outline how your data and work meets funder requirements and how you will manage your data. It’s important to emphasize the purpose of the research and how the data will be generated, collected, and managed. It’s also important to talk about the access and reusability of the data. Detailed instructions can be found here: https://libraries.mit.edu/data-management/plan/write/.