Modular process plants, built from Process Equipment Assembly (PEA), promise a higher flexibility compared to monolithic plants. Digital documentation is a key requirement for a seamless orchestration of a modular plant using PEAs from different vendors. From a process engineering functional view the Module Type Package (MTP) documents the capabilities realized by a PEA. From a automation perspective the documentation and specification can be optimized by utilizing a standard called System Control Diagrams (SCDs). There is up to now no connection of the individual standards. This connection could enable an integrated engineering approach to raise consistency and reduce engineering effort. This work presents an approach to map SCD based automation planning to the MTP. Therefore, both standards are introduced and a mapping from SCD to MTP is realized. It is shown, that most of the functions from SCD have a representation in the MTP, enabling the linking of basic automation functions to capabilities. This enables engineers which are using SCD as a planning tool to efficiently provide an MTP for PEAs or modular plants.

SUMMARY: Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein-DNA complexes. SASA-based approximations underestimated protein-DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. AVAILABILITY AND IMPLEMENTATION: A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Standardization of data models in automation industry is a tedious, time-consuming and multidisciplinary process. The absence of a successfully standardized and established data exchange methodology for PCE (Process Control Equipment) Requests as the most informative capsule of data is an unsolved gap between process and control engineering tools. This contribution describes the first application of a novel and agile standardization method, applied by means of PCE Requests. In the result, within 10 month, leading CAE tool vendors and users of engineering tools have developed a detailed standard electronic data model of the PCE Request, as well as prototype exporter and importer for process and control engineering tools. Consequently, the bidirectional data exchange of PCE Requests between multiple software tools in various disciplines have been successfully demonstrated at the NAMUR Annual General Meeting 2014.

UNLABELLED: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein-DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction. AVAILABILITY AND IMPLEMENTATION: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The interaction between business processes and technical processes is getting more and more important. Throughout this paper, we present how concepts that are used in automation technology can be transferred into concepts that are suitable for use in business process modeling, too. An important aspect is the description of the procedures which have to be executed. In contrast to technical systems, humans as executing agents can, but do not have to follow predefined procedures due to their ability to use their knowledge to work independently in different situations. In a second part, the paper discusses the generation of business processes by project business processes on a meta model, and provides a reference model for a project business layer model.

The P&I diagram (P&ID) shows the product flow structure and the functionality of a process plant. These data are a central base of the downstream control engineering and maintenance processes. We present a model to store these data electronically. Furthermore, the model allows a simple, formal, and unambiguous exchange of P&ID information. It is a bridge between significant information gaps through the information flow between process plant engineering and control engineering. The model is designed in a simple, formal, and unambiguous way. It allows an explicit access to the structural and functional information of the plant. Via this access, the downstream engineering processes can be supported by automatic assistance functions and self-configuration tools. A PandIX model can be created via an XSL transformation, which creates a CAEX file out of a vendor-specific XML file.