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 and a recipe database, a request to execute a step of a unit operation related to preparing an assay, wherein the unit operation defines one or more steps to be performed in a recipe comprising a sequence of unit operations representing a bioprocess, and wherein the unit operation is stored in the recipe database (“stored unit operation”);
generating a first worksheet parameterized by a first set of parameters of the stored unit operation and having an assay user interface comprising a visualization of a plate of the assay to be prepared and initializing a first corresponding electronic laboratory notebook object in the electronic laboratory notebook database associated with the first worksheet having the assay user interface for the assay to be prepared, wherein the first corresponding electronic laboratory notebook object is generated from the step of the stored unit operation related to preparing the assay based on the first set of parameters for the stored unit operation and is associated with the stored unit operation as a persistent record by the electronic laboratory notebook database;
receiving, by the plurality of computers in the distributed laboratory execution platform system, execution data entered into the assay user interface for the prepared assay;
updating, in the electronic laboratory notebook database, the first corresponding electronic laboratory notebook object for the first worksheet having the assay user interface using the execution data for the prepared assay;
in response to receiving an indication that a next step of the unit operation has been initiated:
automatically populating, using the electronic laboratory notebook database, the execution data for the prepared assay into a second worksheet parameterized by the first set of parameters for the stored unit operation and having a second user interface corresponding to the next step of the unit operation; and
initializing a second corresponding electronic laboratory notebook object as a persistent record in the electronic laboratory notebook database associated with the second worksheet having the second user interface, wherein the second corresponding electronic laboratory notebook object comprises the execution data for the prepared assay from the first corresponding electronic laboratory notebook object.
2 . The method of claim 1 , wherein the assay user interface is configured to update the visualization of the plate of the assay to represent contents of one or more wells of the plate in the prepared assay in response to receiving execution data indicating the contents used for filling in each well of the plate.
3 . The method of claim 1 , wherein the step of the unit operation related to preparing the assay is associated with a registered plate template by the recipe database, and wherein the plate template has been registered through operations comprising:
configuring the plate template by assigning (i) one or more planned materials to each well of the plate template, and (ii) labels corresponding to the one or more planned materials assigned to each well.
4 . The method of claim 3 , wherein the one or more planned materials comprise buffer and samples available for preparing the assay as indicated by buffer and samples present in a database that stores up-to-date information about a state of a laboratory.
5 . The method of claim 3 , wherein generating the assay user interface comprises:
determining the one or more planned materials for filling each well of the plate from the plate template registered as the step that is associated with the stored unit operation; and
generating a representation of one or more of the planned materials to be used for filling each well of the plate in the visualization of the plate of the assay.
6 . The method of claim 3 , further comprising:
receiving execution data comprising variant data, wherein the variant data indicates a deviation from the one or more planned materials used for filling at least one well of the plate.
7 . The method of claim 1 , further comprising:
in response to a request, accessing the first corresponding electronic laboratory notebook object in the electronic laboratory notebook database associated with the prepared assay.
8 . 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 plurality of computers, to cause the plurality of computers to perform operations comprising:
receiving, by the distributed laboratory execution platform system comprising a plurality of computers maintaining an electronic laboratory notebook database and a recipe database, a request to execute a step of a unit operation related to preparing an assay, wherein the unit operation defines one or more steps to be performed in a recipe comprising a sequence of unit operations representing a bioprocess, and wherein the unit operation is stored in the recipe database (“stored unit operation”);
generating a first worksheet parameterized by a first set of parameters of the stored unit operation and having an assay user interface comprising a visualization of a plate of the assay to be prepared and initializing a first corresponding electronic laboratory notebook object in the electronic laboratory notebook database associated with the first worksheet having the assay user interface for the assay to be prepared, wherein the first corresponding electronic laboratory notebook object is generated from the step of the stored unit operation related to preparing the assay based on the first set of parameters for the stored unit operation and is associated with the stored unit operation as a persistent record by the electronic laboratory notebook database;
receiving, by the plurality of computers in the distributed laboratory execution platform system, execution data entered into the assay user interface for the prepared assay;
updating, in the electronic laboratory notebook database, the first corresponding electronic laboratory notebook object for the first worksheet comprising the assay user interface using the execution data for the prepared assay; and
in response to receiving an indication that a next step of the unit operation has been initiated:
automatically populating, using the electronic laboratory notebook database, the execution data for the prepared assay into a second worksheet parameterized by the first set of parameters for the stored unit operation and having a second user interface corresponding to the next step of the unit operation; and
initializing a second corresponding electronic laboratory notebook object as a persistent record in the electronic laboratory notebook database associated with the second worksheet having the second user interface, wherein the second corresponding electronic laboratory notebook object comprises the execution data for the prepared assay from the first corresponding electronic laboratory notebook object.
9 . The system of claim 8 , wherein the assay user interface is configured to update the visualization of the plate of the assay to represent contents of one or more wells of the plate in the prepared assay in response to receiving execution data indicating the contents used for filling in each well of the plate.
10 . The system of claim 8 , wherein the step of the unit operation related to preparing the assay is associated with a registered plate template by the recipe database, and wherein the plate template has been registered through operations comprising:
configuring the plate template by assigning (i) one or more planned materials to each well of the plate template, and (ii) labels corresponding to the one or more planned materials assigned to each well.
11 . The system of claim 10 , wherein the one or more planned materials comprise buffer and samples available for preparing the assay as indicated by buffer and samples present in a database that stores up-to-date information about a state of a laboratory.
12 . The system of claim 10 , wherein generating the assay user interface comprises:
determining the one or more planned materials for filling each well of the plate from the plate template registered as the step that is associated with the stored unit operation; and
generating a representation of one or more of the planned materials to be used for filling each well of the plate in the visualization of the plate of the assay.
13 . The system of claim 10 , further comprising:
receiving execution data comprising variant data, wherein the variant data indicates a deviation from the one or more planned materials used for filling at least one well of the plate.
14 . The system of claim 8 , further comprising:
in response to a request, accessing the first corresponding electronic laboratory notebook object in the electronic laboratory notebook database associated with the prepared assay.
15 . One or more computer readable media storing instructions that are executable by a processing device, and upon such execution cause the processing device to perform operations comprising:
receiving, by a distributed laboratory execution platform system comprising a plurality of computers maintaining an electronic laboratory notebook database and a recipe database, a request to execute a step of a unit operation related to preparing an assay, wherein the unit operation defines one or more steps to be performed in a recipe comprising a sequence of unit operations representing a bioprocess, and wherein the unit operation is stored in the recipe database (“stored unit operation”);
generating a first worksheet parameterized by a first set of parameters of the stored unit operation and having an assay user interface comprising a visualization of a plate of the assay to be prepared and initializing a first corresponding electronic laboratory notebook object in the electronic laboratory notebook database associated with the first worksheet having the assay user interface for the assay to be prepared, wherein the first corresponding electronic laboratory notebook object is generated from the step of the stored unit operation related to preparing the assay based on the first set of parameters for the stored unit operation and is associated with the stored unit operation as a persistent record by the electronic laboratory notebook database;
receiving, by the plurality of computers in the distributed laboratory execution platform system, execution data entered into the assay user interface for the prepared assay;
updating, in the electronic laboratory notebook database, the first corresponding electronic laboratory notebook object for the first worksheet having the assay user interface using the execution data for the prepared assay;
in response to receiving an indication that a next step of the unit operation has been initiated:
automatically populating, using the electronic laboratory notebook database, the execution data for the prepared assay into a second worksheet parameterized by the first set of parameters for the stored unit operation and having a second user interface corresponding to the next step of the unit operation; and
initializing a second corresponding electronic laboratory notebook object as a persistent record in the electronic laboratory notebook database associated with the second worksheet having the second user interface, wherein the second corresponding electronic laboratory notebook object comprises the execution data for the prepared assay from the first corresponding electronic laboratory notebook object.
16 . The computer readable media of claim 15 , wherein the assay user interface is configured to update the visualization of the plate of the assay to represent contents of one or more wells of the plate in the prepared assay in response to receiving execution data indicating the contents used for filling in each well of the plate.
17 . The computer readable media of claim 15 , wherein the step of the unit operation related to preparing the assay is associated with a registered plate template by the recipe database, and wherein the plate template has been registered through operations comprising:
configuring the plate template by assigning (i) one or more planned materials to each well of the plate template, and (ii) labels corresponding to the one or more planned materials assigned to each well.
18 . The computer readable media of claim 17 , wherein the one or more planned materials comprise buffer and samples available for preparing the assay as indicated by buffer and samples present in a database that stores up-to-date information about a state of a laboratory.
19 . The computer readable media of claim 17 , wherein generating the assay user interface comprises:
determining the one or more planned materials for filling each well of the plate from the plate template registered as the step that is associated with the stored unit operation; and
generating a representation of one or more of the planned materials to be used for filling each well of the plate in the visualization of the plate of the assay.
20 . The computer readable media of claim 17 , further comprising:
receiving execution data comprising variant data, wherein the variant data indicates a deviation from the one or more planned materials used for filling at least one well of the plate.