Abstract: 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.

Abstract: Methods, systems, and apparatus, including computer programs encoded on computer storage media, for a computing platform that supports bioprocess design, execution, analysis, and technology transfer. One of the methods includes receiving, by a bioinformatics platform from a production facility, a facilities specification that represents properties and capabilities of each item of equipment of a plurality of items of equipment at the production facility. A selection of a recipe to be transferred to the production facility as a production plan is received. A matching process is performed between unit operations of the selected recipe and equipment represented by the facilities specification to convert each equipment-agnostic unit operation of the recipe into an equipment-specific production task to be performed by a particular item of equipment in the production facility. A production plan is generated having a plurality of equipment-specific production tasks for the production facility.

Abstract: 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.

Abstract: Methods, systems, and apparatus, including computer programs encoded on computer storage media, for searching chemical structures. One of the methods includes receiving a fingerprint map for each chemical structure of a collection of chemical structures, generating an inverted index for the collection of chemical structures, receiving a request to search the inverted index for matching chemical structures, obtaining a query fingerprint for the query structure, computing a minimum number of bits and a maximum number of bits that must be present in respective fingerprints of candidate structures in the collection of chemical structures in order for a candidate structure to be considered a match for the query structure, and traversing the inverted index to identify candidate structures having fingerprints with a number of bits in between the minimum number of bits and the maximum number of bits.

Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for updating a molecular database. In one aspect, a method comprises: receiving a request to update a target molecule component stored in the molecular database; updating the data defining a target molecule represented by the target molecule component; identifying a set of target component links that reference the target molecule component; identifying, for each of the target component links, a respective validation criterion associated with the target component link; determining, for each of the target component links, a new validation status for the target component link by evaluating the validation criterion associated with the target component link; and updating the current validation status of each target component link to the new validation status for the target component link.