Department of Computer Science Activity 1998-2004

This report summarizes much of the research and teaching activity of the Department of Computer Science at Dartmouth College between late 1998 and late 2004. The material for this report was collected as part of the final report for NSF Institutional Infrastructure award EIA-9802068, which funded equipment and technical staff during that six-year period. This equipment and staff supported essentially all of the department\u27s research activity during that period

WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar

Transcription factor (TF) binding sites or motifs (TFBMs) are functional cis-regulatory DNA sequences that play an essential role in gene transcriptional regulation. Although many experimental and computational methods have been developed, finding TFBMs remains a challenging problem. We propose and develop a novel dictionary based motif finding algorithm, which we call WordSpy. One significant feature of WordSpy is the combination of a word counting method and a statistical model which consists of a dictionary of motifs and a grammar specifying their usage. The algorithm is suitable for genome-wide motif finding; it is capable of discovering hundreds of motifs from a large set of promoters in a single run. We further enhance WordSpy by applying gene expression information to separate true TFBMs from spurious ones, and by incorporating negative sequences to identify discriminative motifs. In addition, we also use randomly selected promoters from the genome to evaluate the significance of the discovered motifs. The output from WordSpy consists of an ordered list of putative motifs and a set of regulatory sequences with motif binding sites highlighted. The web server of WordSpy is available at

Effects of Offshore Oil and Gas Development: A Current Awareness Bibliography

This bibliography is a compilation of current publications (citations with abstracts) from a wide variety of electronic and print information sources relating to offshore oil and gas development. Subject categories covered include: Biology: Ecological, anatomical, and physiological effects of oil and/or gas, Species as biomarkers, PAH uptake and bioaccumulation, etc. Chemistry/Geochemistry/Geology: Biochemistry, Biodegradation, Bioremediation, Hydrocarbon degradation, Environmental sampling, Soil contamination, etc. Engineering/Physics: Technological advancements in facility/equipment design and use, Spill response and recovery equipment, Physical properties of oil and gas, etc. Environment/Ecosystem Management/Spills: Environmental assessment and management, Oil and/or gas spill description and analysis, etc. Socioeconomic/Regulation/General: Social and economic ramifications, Politics, Governmental policy and legislation, Organizational policy, General interest, etc

Annual Report of the University, 1994-1995, Volumes 1-4

DEMONSTRATING THE STRENGTH OF DIVERSITY A walk around the UNM campus as students change classes demonstrates UNM\\u27s commitment to diversity. Students and professors from a variety of ethnic backgrounds crowd the sidewalks and fill classrooms. Over the past year UNM moved forward with existing and new programs to interest more minority students, faculty and staff in the University and to aid in their success while here. Hispanic Outlook in Higher Education recently recognized the University\\u27s endeavors, ranking UNM as one of the best colleges in the nation at graduating Hispanic students. Provost Mary Sue Coleman says diversity contributes to a stimulating environment where faculty and students have different points of view and experiences. The campus becomes a more intellectually alive place, she says. The efforts to build a diverse campus go hand in hand with the University\\u27s goals of achieving academic excellence and attracting the best and brightest. MINORITY ENROLLMENT In the fall of 1994 a total of 32 percent of the student body came from underrepresented groups. The UNM School of Law had the largest number of Native Americans enrolled in any law school in the country

Annual Report of the University, 2000-2001, Volumes 1-4

Message from the President Thank you for joining me in this look back over the past year at the University of New Mexico. It was a year filled with activity, accomplishment and challenge, and this is our opportunity to reflect back on that year. In 2000-2001 we engaged in a University-wide strategic planning process that called on the energies and talents of hundreds of individuals- faculty, staff, students and members of our broader community. The plan, which will be completed in Fall 2001, will serve as our roadmap for the future and will guide our efforts to capitalize on the opportunities and to meet the challenges of the next several years. This process has encouraged us to examine closely our mission and our values, who we are and what we aspire to become. It has given us reason to be proud of our past and cause to think seriously about how we must change in the future. While this was a year for looking ahead, it was also a year of significant accomplishment. For example, we launched a comprehensive set of programs designed to enrich the academic and social experiences of our undergraduate students. We began the implementation of Freshman Learning Communities where small cohorts of students study and learn together in a common set of courses under the guidance of a senior faculty scholar. We reorganized our advisement systems, we undertook the construction or renovation of student-centered facilities on campus, and we created new support systems to enhance student academic success. It was a year in which our support of faculty, staff and students was our highest priority. Through the support of the New Mexico Legislature, faculty and staff received significant salary increases. A new health benefits plan for graduate assistants was implemented. Our Staff as Students program enabled more than 40 staff members to obtain UNM degrees. And, a Center for Scholarship in Teaching and Learning was established to assist faculty in their efforts to develop more effective teaching skills. Finally, this was a year in which UNM dramatically expanded its role in the local community and throughout the state. Never before has the University been as active or as visible in meeting its public responsibility as it was in 2000-2001. From its active participation in economic development initiatives, to its involvement in K-12 educational improvement efforts, to its significant leadership role in health care delivery, UNM demonstrated its ability to help the state meet its most pressing social challenges. And, as UNM took on a more visible role in supporting the state\\u27s citizens, the support for UNM was returned in kind. This year, annual giving to the University rose to a record 35.3 million dollars, a 40% increase over just two years ago. All told, it has been a gratifying and successful year. However, we cannot allow our past accomplishments to mask the continued challenges facing this University. Neither will we allow these challenges to dominate our thinking and diminish out pride in what the University has achieved. So we will savor our successes and continue to move forward. As always, we thank you for sharing our dreams and for supporting the University of New Mexico. Sincerely, William C. Gordon, Presiden

Advocate 1999-2000 volume 16 number 2

https://digital.sandiego.edu/law_advocate/1036/thumbnail.jp

El mundo de las ciencias de la complejidad

La situación es verdaderamente apasionante. Mientras que en el mundo llamado real –y entonces se hace referencia a dominios como la política, la economía, los conflictos militares y sociales, por ejemplo–, la percepción natural –digamos: de los medios y la opinión pública– es que el país y el mundo se encuentran en condiciones difíciles; en algunos casos, dramática; y en muchas ocasiones trágica, en el campo del progreso del conocimiento asistimos a una magnífica vitalidad. Esta vitalidad se expresa en la ciencia de punta y, notablemente, en las ciencias de la complejidad. Mientras que la ciencia normal –para volver a la expresión de Kuhn– se encuentra literalmente a la defensiva en numerosos campos, temas y problemas –digamos, a la defensiva con respecto al decurso de los acontecimientos y a las dinámicas del mundo contemporáneo–, en el contexto del estudio de los sistemas complejos adaptativos asistimos a una vitalidad que es prácticamente desconocida para la corriente principal de académicos –independientemente de los niveles en los que trabajan–, de científicos, de administradores de educación y de ciencia y tecnología (por ejemplo rectores, vicerrectores, decanos, directores de departamentos, tomadores de decisión, políticos y gobernantes). La corriente principal del conocimiento (mainstream) desconoce una circunstancia, un proceso, una dinámica que sí es conocida por parte de quienes trabajan e investigan activamente en el campo de las ciencias de la complejidad

Alfred P. Sloan Foundation - 2005 Annual Report

Contains program information, grantee profiles, grants list, and financial statements

Education in the Systems Sciences An Annotated Guide to Education and Research Opportunities in the Sciences of Complexity

Comprehensive when it was published in 1990, this guide brought together information on the broad spectrum of education and research opportunities then available in the sciences of complexity. Its purpose was to make these kinds of investigations more accessible by providing information on programs, institutions, organizations, and literature where one can learn about their principles, methods, and applications. The guide was intended to help interested students and educators locate the various academic fields, departments, institutes, and programs that offer education in systems thinking and complex systems research. The guide also served professionals who are already involved in the systems sciences as a directory to general activity in what are otherwise widely separate fields. By browsing the guide one can get a snapshot of where education and research in systems science was happening at the time in both North America and Europe. The landscape has since massively changed so its value is mostly historical