Building Software for Chemistry Labs with Java

airhacks.fm podcast with adam bien

An airhacks.fm conversation with Stanislav Bashkyrtsev (@sbashkirtsev) about:

scientific software for chemists and drug discovery, peaksel flagship software for analyzing mass spectrometer data, parsing binary instrument formats up to gigabytes in size, mass spectrometry measuring molecular weights using electric fields and detectors, daltons as mass units, isotope patterns for molecule identification, storing experimental data in PostgreSQL with potential big data challenges, S3 storage solutions, drug discovery process from hit identification to molecule modifications, molecular libraries and combinatorial chemistry, enumeration of molecular structures in computers, synthesis reactions mixing reactants with solvents and various conditions, liquid handlers and laboratory automation challenges, return on investment issues in early drug discovery automation, lab of the future concepts, Molbrett product combining excalidraw with chemical structure drawing capabilities, SMILES format for representing molecular structures as strings, graph-based molecular formats storing atom connections and bond types, 2D vs 3D molecular visualization preferences, Meve centralized event system for tracking molecular experiments across different software systems, ETL processes for data integration, Crystalline software for documenting protein crystallography experiments, protein structure determination using X-ray crystallography, Synchrotron facilities for high-energy X-ray generation, crystal growing conditions and documentation, fishing crystals with microscope and lasso wands, liquid nitrogen cooling for crystal preservation, Java backend, JavaScript frontend, minimal dependencies approach, six-person team structure, sponsorship business model for open source scientific software development, free updates for sponsors, subscription model for non-sponsors, checkout: https://elsci.io

Stanislav Bashkyrtsev on twitter: @sbashkirtsev