Bioprocess execution workflow interfaces
Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for automatic or semi-automatic bioprocess design, execution, and analysis. In one aspect, a system comprises receiving a request to execute a sequence of unit operations specified by a recipe representing a bioprocess, wherein each unit operation defines one or more steps to be performed, generating, for each step of each unit operation, a worksheet representing laboratory effects of performing the step and having a worksheet interface for displaying bioprocess data and receiving execution data, including initializing, for each worksheet, a corresponding electronic laboratory notebook object in an underlying electronic laboratory notebook subsystem, receiving execution data entered into the worksheet interface for a particular step of a first unit operation, and updating, in the electronic laboratory notebook subsystem, the corresponding electronic laboratory notebook object using the execution data.
1. A computer-implemented method comprising:
receiving, by a distributed laboratory execution platform system comprising a plurality of computers maintaining an electronic laboratory notebook database, a request to execute a sequence of unit operations specified by a recipe representing a bioprocess, wherein each unit operation defines one or more steps to be performed;
generating, for each step of each unit operation, a worksheet for each step of each unit operation representing laboratory effects of performing the step and having a worksheet interface for displaying bioprocess data and receiving execution data, including initializing, for each worksheet, a corresponding electronic laboratory notebook object in the electronic laboratory notebook database, wherein each corresponding electronic laboratory notebook object is generated from a step of a particular stored unit operation and is associated with the particular stored unit operation by the electronic laboratory notebook database;
receiving, by the plurality of computers in the distributed laboratory execution platform system, execution data entered into the worksheet interface for a particular step of a first unit operation;
updating, in the electronic laboratory notebook database, the corresponding electronic laboratory notebook object using the execution data; and
in response to receiving an indication that a next step of the first unit operation has been initiated, automatically populating one or more of bioprocess data or execution data of a second worksheet corresponding to the next step of the first unit operation using the electronic laboratory notebook database.
2. The method of claim 1 , wherein updating the corresponding electronic laboratory notebook object further comprises updating a plurality of corresponding electronic laboratory notebook objects in the electronic laboratory notebook database using the execution data.
3. The method of claim 1 , further comprising:
receiving variant data that relates to at least one step of the sequence of unit operations specified by the recipe; and
generating the worksheet representing laboratory effects of performing the at least one step in accordance with the variant data.
4. The method of claim 1 , further comprising:
receiving an indication that a final step of the first unit operation has been concluded;
in response, automatically initiating a first step of a second unit operation.
5. The method of claim 1 , wherein automatically populating execution data of the second worksheet comprises:
obtaining data readings from one or more laboratory equipment systems; and
populating fields in the second worksheet corresponding to the obtained data readings.
6. The method of claim 1 , wherein automatically populating bioprocess data comprises:
obtaining data from a database that stores up-to-date information about a state of a laboratory; and
populating fields in the second worksheet corresponding to the obtained data.
7. The method of claim 6 , wherein the data represents up-to-date inventory information about one or more input materials to the bioprocess.
8. The method of claim 1 , wherein automatically populating the execution data comprises:
obtaining output data for the particular step of the first unit operation; and
populating the second worksheet with the output data.
9. The method of claim 1 , wherein the execution data comprises container transfer information representing substances transferred from one container to another.
10. The method of claim 1 , wherein the electronic laboratory notebook object is compatible with one or more other electronic laboratory notebook systems.
11. The method of claim 10 , wherein the electronic laboratory notebook object is accessed using the one or more other electronic laboratory notebook systems.
12. The method of claim 10 , wherein the corresponding worksheet interface for displaying bioprocess data and receiving execution data is rendered on a user device that does not have access to the underlying electronic laboratory notebook database.
13. The method of claim 1 , further comprising:
receiving, through a user-interface comprising a set of unit operation objects and one or more links for connecting unit operation objects, the sequence of unit operations specified by the recipe representing the bioprocess through an arrangement of the unit operations into an order using the one or more links;
receiving corresponding data comprising one or more of material inputs, material outputs, bioprocess parameters, equipment, and steps for each unit operation object; and
storing each of the unit operations in the sequence of unit operations specified by the recipe representing the bioprocess and the corresponding data in the electronic laboratory notebook database.
14. The method of claim 1 , wherein the worksheet interface for displaying bioprocess data and receiving execution data comprises:
a steps panel comprising a set of tabs, wherein each tab represents a step in the unit operation, and wherein a particular tab is highlighted as a particular step selected from the unit operation;
a notebook panel corresponding with the selected step, wherein the notebook panel is juxtaposed with the steps panel, and the notebook panel includes:
a text display portion comprising instructions for the step,
a table display portion comprising one or more of a material inputs table, a bioprocess parameter table, or an equipment table for displaying data pertaining to performing the step from the corresponding electronic laboratory notebook object and receiving execution data pertaining to the execution of the step by a user,
an assay display portion comprising a representation of contents of one or more wells of an assay plate, or
a results display portion for receiving and displaying results.
15. The method of claim 14 , wherein the text display portion further comprises rich-formatted instructions for the step.
16. The method of claim 1 , further comprising:
in response to a user request, accessing a particular laboratory notebook object using the electronic laboratory notebook database; and
providing the particular laboratory notebook object for display on a user device.
17. The method of claim 16 , further comprising receiving an indication of validation for the particular laboratory notebook object from the user device.
18. The method of claim 1 , wherein receiving execution data entered into the worksheet interface for a particular step of a first unit operation comprises:
receiving execution data from a first user device displaying the worksheet interface; and
receiving execution data from a second user device displaying the worksheet interface.
19. A distributed laboratory execution platform system comprising a plurality of computers maintaining an electronic laboratory notebook database and one or more storage devices storing instructions that are operable, when executed by the one or more computers, to cause the one or more computers to perform operations comprising:
receiving, by the distributed laboratory execution platform system, a request to execute a sequence of unit operations specified by a recipe representing a bioprocess, wherein each unit operation defines one or more steps to be performed;
generating, for each step of each unit operation, a worksheet for each step of each unit operation representing laboratory effects of performing the step and having a worksheet interface for displaying bioprocess data and receiving execution data, including initializing, for each worksheet, a corresponding electronic laboratory notebook object in the electronic laboratory notebook database, wherein each corresponding electronic laboratory notebook object is generated from a step of a particular stored unit operation and is associated with the particular stored unit operation by the electronic laboratory notebook database;
receiving, by the plurality of computers in the distributed lab execution platform system, execution data entered into the worksheet interface for a particular step of a first unit operation;
updating, in the electronic laboratory notebook database, the corresponding electronic laboratory notebook object using the execution data; and
in response to receiving an indication that a next step of the first unit operation has been initiated, automatically populating one or more of bioprocess data or execution data of a second worksheet corresponding to the next step of the first unit operation using the electronic laboratory notebook database.