The present invention relates to a computer implemented method performed by a device (600) configured to synthesize molecules, wherein the synthesizing comprises performing cycles of a plurality of process steps (PS1-PS4), wherein the synthesizing is controlled by blocks of parameters, the method comprising receiving an indication of a target molecule, generating a synthesizing process description (300) by generating a plurality of blocks (310) of parameters, each block (310) controlling process steps of a respective cycle, receiving user input indicative of modification of the generated plurality of blocks of parameters, modifying the generated plurality of blocks of parameters using the user input, controlling synthesizing of the target molecule by applying the modified plurality of blocks of parameters to control of the respective cycles.

The invention is directed to systems, apparatus and kits for automated synthesis of a plurality of polynucleotides in an array of reaction chambers using a template-free polymerase. In some embodiments, adaptive elements and processes are provided to monitor and control disruption of the synthesis process and fluid movement by enzyme aggregation.

A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. The method also includes sequencing the synthesized or amplified one or more nucleic acid fragments on the substrate. The sequencing may provide feedback to designs of the one or more nucleic acid fragments. The method further includes harvesting the synthesized or amplified one or more nucleic acid fragments based on sequencing. The synthesized or amplified one or more nucleic acid fragments may be assembled to generate a target nucleic acid.

The invention is directed to systems, apparatus and kits for automated synthesis of a plurality of polynucleotides in an array of reaction chambers using a template-free polymerase. In some embodiments, adaptive elements and processes are provided to monitor and control disruption of the synthesis process and fluid movement by enzyme aggregation.

A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. The method also includes sequencing the synthesized or amplified one or more nucleic acid fragments on the substrate. The sequencing may provide feedback to designs of the one or more nucleic acid fragments. The method further includes harvesting the synthesized or amplified one or more nucleic acid fragments based on sequencing. The synthesized or amplified one or more nucleic acid fragments may be assembled to generate a target nucleic acid.

A system includes a nucleic acid amplification module configured to receive deoxyribonucleic acid (DNA) template and to generate a nucleic acid product from the DNA template utilizing an amplification reaction while performing real-time inline monitoring of the amplification reaction via a plurality of sensors. The system also includes a purification module configured to purify the nucleic acid product. The nucleic acid amplification module and the purification module are each automated and form a functionally closed system.

Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

A parallel multi-step bio-reaction system(10) comprising: (a) a substrate arrangement(12) comprising a plurality of bio-reaction substrate holders(18) configured to hold a plurality of bio-reaction substrates(20); (b) a well arrangement(14) comprising a plurality of fluidic wells(22), the fluidic wells(22) corresponding to a plurality of steps of a multi-step bio-reaction; (c) an actuator(16) configured to: (i) move either the substrate arrangement(12) or the well arrangement(14) relative to the other of the substrate arrangement(12) or the well arrangement(14) to change the alignment of the bio-reaction substrates(20) as a group relative to the fluidic wells(22) as a group; and (ii) bring the bio-reaction substrates(20) into and out of contact with fluids in the fluidic wells(22).