Measuring sustainability of seed-funded earth science informatics projects.

Short term funding is a common funding model for informatics projects. Funders are interested in maximizing the sustainability and accessibility of the outputs, but there are no commonly accepted practices to do so in the Earth sciences informatics field. We constructed and applied a framework for sustainability drawing from other disciplines that have more published work focusing on sustainability of projects. This framework had seven sustainability influences (outputs modified, code repository used, champion present, workforce stability, support from other organizations, collaboration/partnership, and integration with policy), and three ways of defining sustainability (at the individual-, organization-, and community-level). Using this framework, we evaluated outputs of projects funded by the U.S. Geological Survey's Community for Data Integration (CDI). We found that the various outputs are widely accessible, but not necessarily sustained or maintained. Projects with most sustainability influences often became institutionalized and met required needs of the community. Even if proposed outputs were not delivered or sustained, knowledge of lessons learned could be spread to build community capacity in a topic, which is another type of sustainability. We conclude by summarizing lessons for individuals applying for short-term funding, and for organizations managing programs that provide such funding, for maximizing sustainability of project outcomes.

Global assessment of technological innovation for climate change adaptation and mitigation in developing world.

Concerns about mitigating and adapting to climate change resulted in renewing the incentive for agricultural research investments and developing further innovation priorities around the world particularly in developing countries. In the near future, development of new agricultural measures and proper diffusion of technologies will greatly influence the ability of farmers in adaptation and mitigation to climate change. Using bibliometric approaches through output of academic journal publications and patent-based data, we assess the impact of research and development (R&D) for new and existing technologies within the context of climate change mitigation and adaptation. We show that many developing countries invest limited resources for R&D in relevant technologies that have great potential for mitigation and adaption in agricultural production. We also discuss constraints including weak infrastructure, limited research capacity, lack of credit facilities and technology transfer that may hinder the application of innovation in tackling the challenges of climate change. A range of policy measures is also suggested to overcome identified constraints and to ensure that potentials of innovation for climate change mitigation and adaptation are realized.

Empirical analysis of retirement pension and IFRS adoption effects on accounting information: glance at IT industry.

This study reviews new pension accounting with K-IFRS and provides empirical changes in liability for retirement allowances with adoption of K-IFRS. It will help to understand the effect of pension accounting on individual firm's financial report and the importance of public announcement of actuarial assumptions. Firms that adopted K-IFRS had various changes in retirement liability compared to the previous financial report not based on K-IFRS. Their actuarial assumptions for pension accounting should be announced, but only few of them were published. Data analysis shows that the small differences of the actuarial assumption may result in a big change of retirement related liability. Firms within IT industry also have similar behaviors, which means that additional financial regulations for pension accounting are recommended.

Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge.

Efficient substructure searching is a key requirement for any chemical information management system. In this paper, we describe the substructure search capabilities of ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson Pharmaceutical Research & Development, L.L.C. The solution consists of several algorithmic components: 1) a pattern mapping algorithm for solving the subgraph isomorphism problem, 2) an indexing scheme that enables very fast substructure searches on large structure files, 3) the incorporation of that indexing scheme into an Oracle cartridge to enable querying large relational databases through SQL, and 4) a cost estimation scheme that allows the Oracle cost-based optimizer to generate a good execution plan when a substructure search is combined with additional constraints in a single SQL query. The algorithm was tested on a public database comprising nearly 1 million molecules using 4,629 substructure queries, the vast majority of which were submitted by discovery scientists over the last 2.5 years of user acceptance testing of ABCD. 80.7% of these queries were completed in less than a second and 96.8% in less than ten seconds on a single CPU, while on eight processing cores these numbers increased to 93.2% and 99.7%, respectively. The slower queries involved extremely generic patterns that returned the entire database as screening hits and required extensive atom-by-atom verification.

Hashing algorithms and data structures for rapid searches of fingerprint vectors.

In many large chemoinformatics database systems, molecules are represented by long binary fingerprint vectors whose components record the presence or absence of particular functional groups or combinatorial features. To speed up database searches, we propose to add to each fingerprint a short signature integer vector of length M. For a given fingerprint, the i component of the signature vector counts the number of 1-bits in the fingerprint that fall on components congruent to i modulo M. Given two signatures, we show how one can rapidly compute a bound on the Jaccard-Tanimoto similarity measure of the two corresponding fingerprints, using the intersection bound. Thus, these signatures allow one to significantly prune the search space by discarding molecules associated with unfavorable bounds. Analytical methods are developed to predict the resulting amount of pruning as a function of M. Data structures combining different values of M are also developed together with methods for predicting the optimal values of M for a given implementation. Simulations using a particular implementation show that the proposed approach leads to a 1 order of magnitude speedup over a linear search and a 3-fold speedup over a previous implementation. All theoretical results and predictions are corroborated by large-scale simulations using molecules from the ChemDB. Several possible algorithmic extensions are discussed.

Bridging the digital divide: reaching vulnerable populations.

The AMIA 2003 Spring Congress entitled "Bridging the Digital Divide: Informatics and Vulnerable Populations" convened 178 experts including medical informaticians, health care professionals, government leaders, policy makers, researchers, health care industry leaders, consumer advocates, and others specializing in health care provision to underserved populations. The primary objective of this working congress was to develop a framework for a national agenda in information and communication technology to enhance the health and health care of underserved populations. Discussions during four tracks addressed issues and trends in information and communication technologies for underserved populations, strategies learned from successful programs, evaluation methodologies for measuring the impact of informatics, and dissemination of information for replication of successful programs. Each track addressed current status, ideal state, barriers, strategies, and recommendations. Recommendations of the breakout sessions were summarized under the overarching themes of Policy, Funding, Research, and Education and Training. The general recommendations emphasized four key themes: revision in payment and reimbursement policies, integration of health care standards, partnerships as the key to success, and broad dissemination of findings including specific feedback to target populations and other key stakeholders.