MathSBML: a package for manipulating SBML-based biological models

Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). Math-SBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml. Supplementary information: Extensive online documentation is available at http://www.sbml.org/mathsbml.html. Additional examples are provided at http://www.sbml.org/software/mathsbml/bioinformatics-application-not

The Evolution of GPLv3 and Contributor Agreements in Open Source Software

Innovation in the computer software industry over the past 15 years increased at a frantic pace thanks in part to the Open Source Software movement. This community of software developers uses legal methodologies to enforce rights and induce others to follow their lead and with openness has come more innovation. The Free Software Foundation’s General Public License (GPL) in particular embodies this spirit and uses a kind of recursive philanthropy or an Open Source-only sandbox, which requires other developers to create their software under licenses with compatible philosophies. How the propagation of these licenses effects innovation in the software industry is the subject of this paper. This inquiry will examine methods used in other industries that embody similar propagation devices from which subsequent Open Source licenses could benefit, proposing that Open Source must balance the risk Open Source companies face with the basic donative intent of the community to continue to offer a cohesive doctrine other developers will continue to follow. In light of the most recent version of the GPL, this paper examines the drafting and revision process the community undertook and will examine what compromises resulted. This process, while a groundbreaking step for the community, necessarily creates new issues to be resolved and may be more reactionary to current events than necessary to support the community’s goals of greater innovation

2016 College Affordability Diagnosis: National Report

College Affordability Diagnosis is the most comprehensive state-by-state study of college affordability since 2008, when the last Measuring Up report was completed by the National Center for Public Policy and Higher Education

Why the Finance Model for Public Higher Education is Broken and Must be Fixed

In order for the U.S. to remain competitive in the 21st-century economy, more individuals are going to need to earn workforce credentials and college degrees. At the same time, however, state governments have been facing financial challenges wrought by chronic structural budget deficits and rising Medicaid expenses, translating into reduced support for higher education. Instead, families now are hard-pressed to shoulder more of the burden of paying for higher education. The current system for financing higher education is broken and needs to be fixed.https://repository.upenn.edu/pennwhartonppi/1020/thumbnail.jp

Structure of a new dense amorphous ice

The detailed structure of a new dense amorphous ice, VHDA, is determined by isotope substitution neutron diffraction. Its structure is characterized by a doubled occupancy of the stabilizing interstitial location that was found in high density amorphous ice, HDA. As would be expected for a thermally activated unlocking of the stabilizing "interstitial," the transition from VHDA to LDA (low-density amorphous ice) is very sharp. Although its higher density makes VHDA a better candidate than HDA for a physical manifestation of the second putative liquid phase of water, as for the HDA case, the VHDA to LDA transition also appears to be kinetically controlled

Evidence for prelocalization of cytoplasmic factors affecting gene activation in early embryogenesis

Differentiation begins early in embryogenesis as different genes become active in different cells. Within the closed system of the early embryo, equal genomes thus direct the creation of diverse cell types. Though the nuclei of these cells contain complete copies of the same genome,(1,2) the nucleoplasmic and cytoplasmic environments of these genomes are not the same, as a result of the distribution of cleavage nuclei into diverse areas of egg cytoplasm early in the cleavage process. In some cases the fate of these nuclei, i.e., the type of differentiated cell to which they or their descendants give rise, has been seen to depend on the area of cytoplasm in which they come to lie

Improved modelling of Siberian river flow through the use of an alternative frozen soil hydrology scheme in a land surface model

A parameterisation to incorporate the effects of frozen soil on modelled hydrology is described and implemented within a land surface model, the Joint UK Land Surface Environment Simulator. It is shown to generally improve the modelled flow of Siberian rivers compared to observations, specifically in seasons of freezing or thawing soil. Most noticeably, the revised model increases the snowmelt flow peak by 26–100% compared to the control model thereby better matching observed flows. The model physics resulting in the changes to river flow are discussed and attention is given to the effect of inaccuracies in snowfall driving data which can hinder the comparison of new model processes

Improving Higher Education Attainment for All Students: A National Imperative

Once a world leader, the United States has fallen behind other nations in the educational attainment of its population. Although the percentage of adults age 45 to 54 who hold at least a baccalaureate degree is higher in the United States than in other Organisation for Economic Co-operation and Development (OECD) nations, the United States now ranks below several other nations, including Norway, the Netherlands, Korea, New Zealand, Denmark, and Sweden, in the share of adults age 25 to 34 who hold this credential. While the U.S. invested heavily in the educational attainment of earlier generations, other nations have been investing substantially in their younger populations. Essentially, educational attainment has stalled in the United States, with about 30% of adults in each age cohort holding at least a bachelor\u27s degree. Over this same period, however, educational attainment has been rising dramatically in some other nations. In Korea, for example, 34% of adults age 25 to 34 now hold at least a baccalaureate degree, up from just 17% of adults age 45 to 54.

Faultlines Shaping Higher Education Policy and Opportunity in California: Executive Summary

We present findings from a case study on California’s higher education sector that explores the relationships between public policy, state contexts, and higher education performance over the past two decades (2000–2020). Through the collection of primary and secondary data, including interviews with 16 policymakers, education policy leaders, and researchers inside and outside of California, we document the development, manifestation, and implications of three primary faultlines: (a) Persistent disparities by race, socioeconomic status, and geography that combine to sharply limit individual educational and economic opportunity for many within the state. Any measure of performance in higher education must address how higher education closes these disparities relative to the magnitude of the disparities in the population. (b) Fragmentation, or the policy-related phenomena and structures that contribute to a lack of alignment and synchronicity in the statewide approach to postsecondary education. (c) Volatility, or extreme variations and unpredictability in state and local funding for higher education, with impacts that extend into institutional resource allocations and family budgets. Our case study documents a need for sustained state policy leadership in higher education or sustained public stewardship of higher education. Year-over-year, session-by-session, and sector-by-sector agreements fall short in addressing the deep faultlines outlined in this report. We make several recommendations for how public policy can begin to address these issues and better meet the needs of the state’s populous