The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

open access articleBackground: The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. Results: We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. Conclusions: This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software

Computer-based tools for supporting forest management. The experience and the expertise world-wide

Report of Cost Action FP 0804 Forest Management Decision Support Systems (FORSYS)Computer-based tools for supporting forest management. The experience and the expertise world-wide answers a call from both the research and the professional communities for a synthesis of current knowledge about the use of computerized tools in forest management planning. According to the aims of the Forest Management Decision Support Systems (FORSYS) (http://fp0804.emu.ee/) this synthesis is a critical success factor to develop a comprehensive quality reference for forest management decision support systems. The emphasis of the book is on identifying and assessing the support provided by computerized tools to enhance forest management planning in real-world contexts. The book thus identifies the management planning problems that prevail world-wide to discuss the architecture and the components of the tools used to address them. Of importance is the report of architecture approaches, models and methods, knowledge management and participatory planning techniques used to address specific management planning problems. We think that this synthesis may provide effective support to research and outreach activities that focus on the development of forest management decision support systems. It may contribute further to support forest managers when defining the requirements for a tool that best meets their needs. The first chapter of the book provides an introduction to the use of decision support systems in the forest sector and lays out the FORSYS framework for reporting the experience and expertise acquired in each country. Emphasis is on the FORSYS ontology to facilitate the sharing of experiences needed to characterize and evaluate the use of computerized tools when addressing forest management planning problems. The twenty six country reports share a structure designed to underline a problem-centric focus. Specifically, they all start with the identification of the management planning problems that are prevalent in the country and they move on to the characterization and assessment of the computerized tools used to address them. The reports were led by researchers with background and expertise in areas that range from ecological modeling to forest modeling, management planning and information and communication technology development. They benefited from the input provided by forest practitioners and by organizations that are responsible for developing and implementing forest management plans. A conclusions chapter highlights the success of bringing together such a wide range of disciplines and perspectives. This book benefited from voluntary contributions by 94 authors and from the involvement of several forest stakeholders from twenty six countries in Europe, North and South America, Africa and Asia over a three-year period. We, the chair of FORSYS and the editorial committee of the publication, acknowledge and thank for the valuable contributions from all authors, editors, stakeholders and FORSYS actors involved in this project

MIS Guidelines for Employment Law Programs in Poland

The guidelines presented in this report propose an efficient architecture for structuring the huge volume of information flow necessary to manage and administer the several labor market programs operated by the SOLO (System of Labor Offices). The proposal includes a recommendation for the sequence of events in developing the many parts of the system which exploits the latest technical and methodological possibilities, but recognizes the practical constraints of time and money. At the heart of the proposed automated management information system (MIS) to support planning, evaluation, and budgeting for labor market programs in Poland is a set of performance indicators. These performance indicators are the main instrument for monitoring the effectiveness of the several programs. The use of performance indicators will allow a standardized assessment of program performance across voivods, local offices, and programs which is not provided by other methods of evaluation