Office Automation And Group Collaboration Software

Office Automation And Group Collaboration Software

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Our group of three within Global Discovery Chemistry at a large Pharmaceutical Company was tasked with implementing a unique and innovative way in which high throughput parallel chemical synthesis could be performed by the traditional bench chemists. Building off the deployment of a new collaborative software system, the Electronic Notebook (ELN) by CambridgeSoft Corporation, our job was to identify a way to develop a back-end system which links the chemist’s notebook to automated synthesis in the Lab. The new Electronic Notebook was established in order to replace existing paper notebooks, making it possible for chemists across the globe to view and otherwise copy, duplicate, or build off experiments of others. The back end platform is custom developed within our group and links to the notebook, by a series of table views, to read inputs and fully automate the process in which parallel chemistry is performed in the Robotics Laboratory. This paper will discuss the collaborative ELN software, as well as the back end custom application for linking the chemist to the Laboratory Automation.

The chemist first identifies a molecule of interest based on prior biological screening assays. Using Computer Aided Drug Design, they then come up with areas of interest in exploring new sets of molecules, building off the one first identified. Next they search a scientific database, including SciFinder or the Electronic Notebook to view established synthesis techniques. Once the initial synthesis protocol is worked out, the chemist will design the library of desired compounds and draw the reaction scheme into their ELN. In addition, the chemist must also identify the scale of reaction or amounts of material of each compound to add, as well as the solvent system and temperature which will best optimize the yield of product formed. Two main benefits for entering the data in this manor include first a permanent electronic record in which others are able to view and search, and second as a portal into running their experiments in an automated fashion using the custom Lab Automation Software we call OtterChem.

One limitation we are currently facing with the ELN is the legality of such an all electronic system and the future ability to defend patents in court for drug discovery. Steps must be taken in order to establish a date of conception, audit trail of entries, and an electronic signature of a witness skilled in the area of chemical synthesis.

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Though we are currently planning to go fully electronic in the future, for now the chemist must still print out their experiments, paste them into a paper notebook, and have them physically witnessed at the bottom of the page... For the OtterChem application, the software was designed for ease of use, however since there are so many possible workflow's, the software’s flexibility must be recognized. The chemist must not be intimidated by using the lab equipment and automation.

Once data is entered into the ELN, the chemist can utilize what we call the Open Access Automation, or the OtterChem software which is integrated with Lab Robotics. Once in the Lab, OtterChem connects to an analytical balance and displays notebook entries for weighing and dilutions of reagents. After the materials are weighed and into solutions, racks of reagents are scanned onto the automated synthesis stations and OtterChem is able to automatically program the robotics for sample mapping into the reaction blocks, based on the original ELN entries. Here the chemicals are automatically mixed and heated until the reaction is complete. The next day, the chemist is able to perform automated sample transfer into Micro Titer Plates for the purpose of purity analysis. The data from the analytical run is automatically brought back into OtterChem for viewing by the chemist at their desk. Samples identified for further purification are scanned into a High Pressure Liquid Chromatography (HPLC) system; and since the device is automatically programmed, the chemist need only address the samples, not programming the instruments. During purification, the material is injected into the system for the purpose of pumping the sample through a packed column containing C-18 material. The desired product, as well as impurities of the reaction, are separated by the packed material and detected by UV254 wavelength at different times across the gradient. When the material exits the column and the UV signal is detected, the instrument is triggered to collect a “fraction tube” of isolated material. In the end, sets of tubes contain isolated product as well as undesired by-products, thus splitting one injection of a crude mixture into several different fraction tubes.

The data is again reviewed in OtterChem and the chemist chooses peaks of interest for analysis through an analytical HPLC-Mass Spectrometer (MS). Since the desired mass is known up-front, an automated analysis is performed and product purity is calculated by the area under the UV peaks. The OtterChem software color codes the fraction wells with green (mass found with desired purity level), yellow (mass found but not exceeding the desired area percent under the curve), or Red (mass not found). At this point the chemist verifies the automated analysis and is ready to transfer the pure products to sample submission tubes.

The transfer of final compounds is once again automatically programmed by the software. Scripts are written to Pick and Place (PNP) empty tubes so they can be tarred on a balance and the barcode can be read. The instrument then maps the desired products into these tubes. After drying of the compounds in a high-speed rotor-evaporator equipped with heat and vacuum, the samples are brought back to the instrument for final compound weight. The weights and purity is automatically sent back to their electronic notebook.

By using collaborative software (ELN) and customized Lab Programming, the chemist is able to take advantage searching others work in the ELN to design their synthesis, and then have the ability to produce those compounds in an automated workflow. Developing this back end automation can give us a competitive advantage over other companies by having the ability to report and obtain data in a fast and efficient manor.
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