EDD User Stories¶
Here we present real EDD user stories and how users interact with EDD.
Proteomic user story¶
- Build a study to hold experiment(s)
- Submit samples for proteomic analysis
- Generate and export worklist for proteomic data acquisition
- Import proteomic data
- Visualize proteomic data
Steps in EDD:
- Create Study
- Drag and drop experiment detail excel file (includes strains/plasmids and meta data - ie shaking speed).
- Generate and export worklist from experiment detail lines.
- Import data from skyline machine.
- Visualize data in line and bar charts with ability to filter data.
Jen’s User Story:
Jennifer is a scientist at JBEI interested in engineering E. coli to produce a biofuel. She chooses a pathway to produce a good biofuel and finds genes for each step in the pathway. She designs her constructs, gets her DNA synthesized by an outside company, assembles the plasmids and transforms them into E. coli. Because she is a good scientist she puts the information regarding the strains and plasmids into the JBEI ICE-registry. Other scientists can then obtain those same strains and plasmids if they are interesting in replicating her experiment. Once she has her biofuel producing organism she measures how much biofuel it makes but it only produces a small amount. She then decides to check for pathway protein production to see if there are any bottlenecks in her pathway. She meets with the Proteomics team to design an experiment to quantify proteins in her strains. Chris tells her that she has to make an EDD study to enable data sharing across JBEI or they won’t run her samples. Jennifer creates a study for her experiments by using the proteomics instructions for the EDD. She adds her experiment details lines to her study along with the experimental metadata (culture conditions, induction conditions, etc…). She lets the Proteomics team know that the samples are ready and that she created a study in the EDD. The Proteomics team looks at the EDD study to understand the samples that are being analyzed and check that any new protein sequences need for the experiments are available.
The Proteomics team prepares the samples for analysis and then exports a Worklist from the EDD study that Jen created for the LC-MS system. After the data is collected the Proteomics team processes the data with Skyline and imports the data into the EDD. The Proteomics team informs Jennifer that her data is available in the EDD, so she goes to her study and visualizes the proteomic data with the awesome graph tool (with error bars coming soon) in the EDD and goes on to win a Nobel prize.
Import Data for a completed experiment¶
- Build a study
- Import data from experiment user has run
- Verify data is correctly imported
- View study data has been imported
- Create study by giving study a name. Optional add description and enter contact for who to contact re experiment.
- Define experimental parameters/settings
- Download template file
- Enter samples and meta data corresponding to experiment.
- Save file
- Drag/drop file into study
- Experiment detail lines are created.
- Import Data
- Select type of file to import a. Generic CSV b. Skyline output c. Gene transcription data (as table fo RPKM values) d. HPLC instrument data file e. Proteomics data f. Mass Distrubution Vector g. Biolector XML
- Drag/drop file
- Verify data (table and graph form)
- Confirm assays correspond to lines created from Experiment Description
- Import data
- View imported data on data tab of Study
- Verify data has been imported
- view graph
- view table
Daniel’s User Story:
Daniel is a scientist. He works at JBEI and he did an experiment on something. Given that he works at JBEI his data is most likely a chromatogram in the form of an Agilent .D file. He’s interested in uploading his data so that he can share his research/data with other scientists. Someone at work told him about the EDD app. He decides to check it out.
After he logs in, he gets to the homepage and the first thing he sees is a button that says “input data”. He clicks on the button “input data” and is taken to a page where there are instructions and options on how to input his data.
First he has to create a new study for his experiment. He then sees that he has to enter the experiment details by downloading a sample template. He enters the shaking speed, etc of the experiments he has already completed for the experiment description file. He also decides to link his electronic notebooks so that others can see more of his protocols. He then looks at the list of available data types and chooses the type of data he would like to input. He chooses the data type and sees “have you put your data in the correct format?” This sentence is a link that expands. When he clicks to expand, he sees examples of the correct way to format his data. He sees that his data is not in the right format and then spends several days analyzing his chromatograms and then typing the results into Excel for normalization and calibration so that it can be uploaded into EDD. Daniel wishes the EDD would actually process raw data sources like chromatograms.
Armed with an excel file now he clicks on his data type. He sees that his data is in the correct format. Wonderful. He sees that he can click and drag his file onto the page. He drags and drops his excel file. He then makes sure all of his lines are input and clicks “looks good. input my data” and he is immediately taken to a screen where he is notified that his information has been successfully uploaded. He sees a graph with his measurements and a table that includes his assays.
Problem Daniel is Facing: Major problem here is that Daniel’s experiment involves a metabolite for which the EDD does not know about, and he needs to be able to add it. Daniel’s experiment also involves a measurement data type that is not already in EDD and he needs to add it (for example 3 gene cluster copy number measurements, every experiment has weird twists and the EDD should handle them flawlessly and intuitively).
- Download data from an experiment
- Navigate to the EDD study of interest
- Search by name, contact, date.
- Search Recent Studies
- Search My Studies
- Select lines to download
- Click export data
- On export page, remove certain columns or leave as is.
- Click download.
- Lines are downloaded with assays and measurements.
Eli’s User Story:
Eli is a scientist interested in running a flux analysis on David’s data. He searches studies based on David’s name. He finds the study he is interested in and clicks on it. He clicks on the table tab. He clicks selects all and clicks export. He is taken to the export page where he can remove unnecessary columns. He then clicks download and views the downloaded data as an excel file.