The efficiency of polymer synthesis is increased by reducing the number of monomer addition cycles needed to create a set of polymer strands. The number of cycles depends on the sequences of the polymer strands and the order in which each type of monomer is made available for addition to the growing strands. Efficiencies are created by grouping the polymer strands into batches such that all the strands in a batch require a similar number of cycles to synthesize. Efficiencies are also created by selecting an order in which the monomers are made available for addition to the growing polymer strands in a batch. Both techniques can be used together. With these techniques, the number of cycles of monomer addition and commensurate reagent use may be reduced by over 10% as compared to naïve synthesis techniques.

Disclosed herein are systems, methods and devices for the continuous production and processing of compounds, including biopharmaceutical compounds. The system and devices are operated in an automated manner and capable of operation under Good Manufacturing Practice (GMP)-compliant conditions.

The present invention discloses a method and apparatus for fully automated iterative polymer synthesis at a large scale.

The invention is directed to methods and apparatus for parallel enzymatic synthesis of polynucleotides in an array of reaction chambers using a tem-plate-free polymerase that has sequence-dependent coupling efficiencies. Whenever sequences causing low efficiency coupling occur at a 3′ end of a growing chain of a polynucleotide being synthesized, one or more additional coupling cy-cies without de-protection steps are inserted into synthesis plans to provide additional time for completing the coupling reaction at that position of the polynucleotide.

A method for executing multiple chemical programs in parallel in an array of chemical reactors using a single array of substance containers may be provided. The method includes receiving a plurality of chemical programs, building a plurality of records comprising each a chemical program. Thereby, each record includes a key and a data field, wherein the key is indicative of the reactants required for the respective chemical reaction, and wherein the data field includes the chemical program. The method further includes creating an ordered data structure of the data records based on the keys, selecting a next record from the ordered data structure, assigning the selected next record to selected ones of the array of chemical reactors, repeating the steps of selecting and assigning until, as a maximum, each chemical reactor has a defined record assigned to it, and executing the chemical programs according to their defined records in parallel.

A method for executing multiple chemical experiments in parallel may be provided. The method comprises receiving a list of actions to be performed for synthesizing a chemical product. Thereby, the actions correspond to at least two chemical partial reactions and the list comprises a delimiter symbol separating two chemical partial reactions, determining identical chemical partial reactions, and building a reaction commonality tree (RCT) of the chemical reactions. Furthermore, the method comprises executing a plurality of the identical chemical partial reactions independent of a sequence of chemical partial reactions of the reaction commonality tree only once. Each of the identical chemical partial reactions is executed in a different chemical reactor and each resulting intermediate product has a quantity of the sum of the related identical chemical partial reactions. The method also comprises, storing the intermediate chemical products in a separate container, and executing remaining chemical partial reactions according to the RCT.

The invention provides a method for preparing a compound or a product having one or more characteristics that meet or exceed a user specification, the process comprising the step of selecting a first combination of chemical inputs, optionally together with physical inputs, and supplying those inputs to a reaction space, thereby to generate a first product; analyzing one or more characteristics of the product generated; comparing the one or more characteristics against a user specification; using a genetic algorithm selecting a second combination of chemical inputs, optionally together with physical inputs, wherein the second combination differs from the first combination, and supplying those inputs to the reaction space, thereby to generate a second product; analyzing one or more characteristics of the second product generated; comparing the one or more characteristics generated against the user specification; repeating the selecting and analyzing steps for further individual combinations of chemical and/or physical inputs, to provide an array of products wherein the flow chemistry system operates continuously to provide the first, second and further products, thereby to identify one or more products meeting or exceeding the user specification.

Systems and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of one or more reaction sites on a first component; providing a material for the one or more reaction sites in one or more surface channels of the first component; connecting the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; and aligning the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component.

Reagents and solvents used for polymer synthesis are reused or recycled rather than discarded. The outflow from each step of polymer synthesis may be collected separately in one of multiple dedicated containers. Reuse returns the outflow from a step of polymer synthesis back to an input of a polymer synthesizer for subsequent use in that same step. Recycling processes the outflow from one or more steps of polymer synthesis to restore original concentrations or purity levels for use in a later synthesis run. Quality control analysis may determine if outflow collected from a polymer synthesizer is reused or recycled. These techniques reduce reagent cost and waste quantity. These techniques may be used with phosphoramidite or enzyme-based synthesis of deoxyribonucleic acid (DNA).

Storage media are provided. A substrate has an array of addressable locations thereon, each addressable location adapted to be physically associated with a collection of molecules, each collection comprising at least a first subcollection of molecules and a second subcollection of molecules. The molecules in the collection are selected from a set of unambiguously identifiable molecules, the set comprising at least a first subset of molecules and a second subset of molecules. Each molecule in the first subset is identifiable by a first physical property, and each molecule in the second subset is identifiable by a second physical property, different from the first physical property. Each molecule in the set is uniquely associated with a predetermined position in a numerical value, wherein the presence of the molecule in the collection indicates a predetermined digit at the associated position and the absence of said molecule in the collection indicates a zero at said associated position.