1. BioBox Documentation
  2. Library Organization and Data Upload

BioBox is Transitioning Samples to Experiments

We are transitioning the library to support important metadata associated with your experiments

Why are we doing this ? 

Moving towards multi-omic support 

  • As we prepare to support key sequencing technologies such as scRNA, ChIP, and ATAC  we want to provide you with the flexibility to better distinguish and organize the data in your library according to experiment type
  • The transition to experiments will enable you to keep track of important metadata such as technical replicates and run type associated with your data

Public Data support 

  • In order to filter through public data and find files that would be relevant to you, we are upgrading the library to consolidate information regarding public data experiments  

What will change? 

  • The "Samples" tab in the library will be transitioned to "Experiments".   Experiments will be categorized according to "Transcriptomics" "Epigenomics" and "Genomics"  
  • Each Sample will be transitioned to an "Experiment" associated with one of your model records.  You will be able to keep track of the Run Type,  Technical Replicates and all of the files associated with each experiment. 
  • When uploading files to your library, you will specify which Experiment in your library they are associated with.
  • Updates to the pipeline file selection process. Files will be organized according to experiment and you will be able to sort though file types to quickly identify the files you are looking for. 
  • A faster and more efficient table to organize and sort data in your library. We have listened to your concerns and have made improvements to all of our tables. 
    Screen Shot 2022-03-09 at 1.21.19 PM

What Actions are Required? 

  • The transition period will take place over the next two weeks during which you will have the opportunity to convert your Samples to Experiments. The transition period will end on March 24th, 2022.
  • Within the library under the "Samples" tab you will see a banner informing you about the transition to Experiments.
Screen Shot 2022-03-09 at 1.40.12 PM
 
    • Select "Convert Samples" and this will take you to a table where you can specify the Experiment Type, Experiment Name, Run Type, and number of Technical Replicates.
      • Screen Shot 2022-03-09 at 1.40.44 PM
    • Once the table has been filled out and you select "Next" the  following page will enable you to assign your FASTQ files to specific technical replicates.
      Screen Shot 2022-03-09 at 1.41.11 PM
  • Once you submit your conversion requests all of the information you have specified will be saved and reflected in the application when the user interface is transitioned to reflect experiments. Only submit this form once. 
  • Please contact your account manager and they will walk you through this process 

What happens if you do not manually convert you samples? 

    • If you do not manually convert your samples, your samples will be auto-converted to experiments as follows 
      • All RNA samples will be converted to Total RNAseq experiments with 1 technical replicate each.
      • All DNA samples will be converted to WGS experiments with 1 technical replicate each.
      • If you have 2 FASTQ files associated with 1 sample the new experiment will be paired end, if you have 1 FASTQ file associated with a sample the new experiment will be single end.
      • If you have three or more FASTQ files associated with a sample, the experiment will have 3 technical replicates and will be single end. 
    • Following the transition period you will have the option to edit/ update all information associated with your experiments. We highly suggest booking a meeting with your account manager to ensure this transition is as smooth as possible.