Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration

The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.

Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a _core metabolic model_ containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an _intermediate metabolic model_ attempts to fill gaps and provides better continuity. Third, a _complete metabolic model_ contains the full set of known metabolic reactions and compounds in _Arabidopsis thaliana_.

We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry

Catalyzing Collaboration: The Developing Infrastructure for Federal Public Private Partnerships

There is growing interest on the part of government, philanthropy and business to work together to achieve greater impact. Partnerships that span the sectors have the potential to achieve more than any sector can achieve on its own by leveraging the strengths of each. However, such partnerships also give rise to added costs and entail greater risks. To address these challenges, offices of strategic partnerships are emerging at the federal level to provide an infrastructure to catalyze cross-sectoral partnerships. This report examines 21 such offices in federal departments and agencies whose purpose is to facilitate and accelerate partnerships with philanthropy and business -- ranging from the Department of Housing and Urban Development and the Department of Education, to the Department of State and the Agency for International Development, to the Department of Homeland Security and the Federal Emergency Management Agency. The formation of these offices has been driven by champions within government -- many with prior experience in philanthropy or business -- that have witnessed the power of working collaboratively with other sectors. Their actions have often been reinforced by executive orders and other directives conducive to their growth. In the case of those offices that have been created in the last few years, they have also been encouraged by the examples of their more established counterparts

Four facets of a process modeling facilitator

Business process modeling as a practice and research field has received great attention in recent years. However, while related artifacts such as models, tools or grammars have substantially matured, comparatively little is known about the activities that are conducted as part of the actual act of process modeling. Especially the key role of the modeling facilitator has not been researched to date. In this paper, we propose a new theory-grounded, conceptual framework describing four facets (the driving engineer, the driving artist, the catalyzing engineer, and the catalyzing artist) that can be used by a facilitator. These facets with behavioral styles have been empirically explored via in-depth interviews and additional questionnaires with experienced process analysts. We develop a proposal for an emerging theory for describing, investigating, and explaining different behaviors associated with Business Process Modeling Facilitation. This theory is an important sensitizing vehicle for examining processes and outcomes from process modeling endeavors

Instructional Materials and Implementation of Next Generation Science Standards: Demand, Supply, and Strategic Opportunities

Next Generation Science Standards (NGSS) are in demand, but the supply of high quality K-12 instructional materials in science is lacking. This disconnect comes at a critical time in the implementation of new science standards, which are now influencing the teaching and learning of more than 50 percent of the students in American schools.  As of spring 2017, 18 states plus the District of Columbia have adopted the NGSS, and 16 states have adapted their state science standards based on the Framework for K-12 Science Education and the NGSS. As part of Carnegie Corporation of New York's Education Program, we have observed the growing need to improve the supply and demand for high quality K-12 instructional materials and professional learning designed for the NGSS. To inform the grantmaking in our Leadership and Teaching to Advance Learning portfolio, the Corporation recently held a convening of science curriculum developers, experts in professional learning, state and district science leaders, and other educators to discuss these challenges

Beyond Green: The Arts as a Catalyst for Sustainability

The creative sector has played a significant role in efforts to raise awareness of the impacts of climate change and encourage sustainable social, economic, and environmental practices worldwide. Many artists and cultural organizations have embarked on remarkable projects that make us reflect on our behaviors, our carbon footprints, and the claims of infinite growth based on finite resources. Sometimes treading a fine line between arts and advocacy, they have sparked extraordinary collaborations that reveal new ways of living together on a shared planet. The 'art of the possible' will become even more relevant as 2016 dawns - bringing the challenge of how to implement the Sustainable Development Goals and the Climate Change Agreement adopted at the end of 2015. Yet with negotiations overshadowed by scientific controversy, political polemic and geographic polarization, individuals can easily lose faith in their own ability to shape change beyond the hyperlocal level. Against this challenging backdrop, could the arts and creative practice become a particle accelerator - to shift mindsets, embrace new ways of sharing space and resources, and catalyze more creative leadership in the public and private spheres? The goal of this Salzburg Global Seminar session was to build on path-breaking cultural initiatives to advance international and cross-sectoral links between existing arts and sustainability activities around the world, encourage bolder awareness-raising efforts, and recommend strategic approaches for making innovative grassroots to scale for greater, longer-term impact

Cracking the Network Code: Four Principles for Grantmakers

As grantmakers and nonprofits are looking for ways to collaborate more effectively, many are experimenting working with and through networks to achieve greater impact. Because networks are by definition loosely controlled and emergent, understanding how to effectively support them feels like a mystery to many grantmakers.GEO's newest publication sets out to crack the code behind the network mystique. In fact, there is a method to working more efficiently and effectively through networks, and a critical first step for grantmakers is adopting a network mindset, which may require dramatic shifts in attitude and behavior for some. "Cracking the Network Code" outlines four principles that comprise the network mindset, illustrates the principles with a range of examples of networks that have achieved real results, and offers practical questions and recommendations to help grantmakers achieve the benefits and avoid common pitfalls of working through networks

Catalyzing Networks for Social Change

Explains how funders can "catalyze" networks to address complex, interconnected issues: weave social ties; access diverse perspectives; openly build and share knowledge; create infrastructure for widespread engagement; and coordinate resources and action

Developing Equity-Centered Leadership Knowledge and Skills via Lesson Study in an Online Mathematics Specialist Program

This paper highlights how coursework within a synchronous online mathematics specialist program enhanced candidates’ leadership knowledge and provided structures that addressed issues of equity and access. A focus on one online assignment grounded in Lesson Study played a pivotal role in developing equity-centered leadership and instructional practices. Program instructors and recent alumni illuminate how designing, implementing, and reflecting on the Lesson Study experience served as a cornerstone for advancing their mathematics instruction in the following ways: (a) as instructors designing an online leadership course, (b) as learners within an online environment, and (c) as educators within their K–8 school settings. The description of these experiences supports the broader mathematics education community’s goal of achieving a cohesive vision for the teaching and learning of mathematics, while promoting equitable practices in school-based work

Knowledge, understanding and the dynamics of medical innovation

This paper investigates the processes by which scientific knowledge is created and legitimized. It focuses on scientific developments in a branch of medicine and explores the pathways through which the growth of knowledge enables advances in medical science and in clinical practice. This work draws conceptually on evolutionary approaches to technological change. The empirical part presents a longitudinal analysis of a database of scientific publications in the field of ophthalmology over a period of 50 years. Such an exercise allows us to identify pathways of shared understanding on a disease area, and to map out distinctive trajectories followed by the ophthalmology research community. The paper also contributes to general understanding of the innovation process by supporting the notion that knowledge coordination is a distributed process that cuts across and connects complementary areas of expertise.