Systems biology, models, and concurrency

Aim/Purpose: The purpose of this study is to identify how Advanced level Mathematics and Mathematics course units offered at university level do impact on the academic performance of theoretical Computer Science course units. Background: In Sri Lankan state universities, students have been enrolled only from the Physical Science stream to do a degree program in Computer Science. In addition to that, universities have been offering some course units in Mathematics to provide the required mathematical maturity to Computer Science undergraduates. Despite of this it is observed that the failure rates in fundamental theoretical Computer Science course units are much higher than other course units offered in the general degree program every year. Methodology : Academic records comprised of all 459 undergraduates from three consecutive batches admitted to the degree program in Computer Science from a university were considered for this study. Contribution: This study helps academics in identifying suitable curricula for Mathematics course units to improve students’ performance in theoretical Computer Science courses. Findings: Advanced level Mathematics does not have any significant effect on the academic performance of theoretical Computer Science course units. Even though all Mathematics course units offered were significantly correlated with academic performance of every theoretical Computer Science course unit, only the Discrete Mathematics course unit highly impacted on the academic performance of all three theoretical Computer Science course units. Further this study indicates that the academic performance of female undergraduates is better than males in all theoretical Computer Science and Mathematics course units. Future Research: Identifying other critical success factors contributing to the students’ academic performance of the theoretical Computer Science through empirical studies

Introduction The computing sciences are complex fields that combine both theoretical and practical components. Students successfully completing an undergraduate computer science program should have instruction in both the mathematical and theoretical foundations of computing as well as the more practical aspects of how to effectively use computers to solve problems. Software engineering, as its name implies, is more directed toward the practical aspects of how to successfully develop complex systems that meet user requirements and are reliable, usable, and maintainable. Computing Curricula 2005 recognizes the need for more extensive education to produce professional engineers than what can be reasonably provided in a typical computer science program (ACM, 2005). As such, they propose engineering be treated as a totally separate discipline within computer science education. However, while there has been some debate about the exact role engineering should have in a computer science program (Curran, 2003), the ACM Curricula has maintained the importance of engineering to all computer science students and has kept it as a core element in computer science education (ACM, 2008). For purposes of this paper, we will focus on the teaching of engineering within the computer science discipline. Unlike other topics in the computer science major, the techniques and principles taught in engineering are often first developed and refined in industry before arriving in the classroom. As commercial development techniques and tools evolve, so pedagogical methodologies change. Computer science educators have taken different approaches to teaching engineering over the years, both as a result of changing methodologies as well as individual beliefs about what teaching methods work best in a particular academic environment. This paper is a case study in applying current productivity tools (specifically Redmine) in a engineering course at our institution. The objectives of the study are to investigate how to integrate the tools into the existing structure and evaluate their impact. We describe our experience in recently changing our approach to teaching engineering to be more aligned with current tools and how to effectively use them in an academic environment. The paper begins with an overview of engineering teaching methods, then describes our traditional approach and motivation for changing, how the new approach was integrated into the course, our experience with the change, and, finally, our plans for the future Software Engineering Education Background Software Engineering is defined as the application of a systematic, disciplined, quantifiable approach to the development, operation and maintenance of software (Petkovic, Thompson, & Todtenhoefer, 2006, p. 294). The need to teach engineering in colleges has been identified for decades. Stiller & LeBlanc (2002) point out as far back as the early 1990's, ACM Computing Curricula suggested that the at least one engineering course should be required in accredited computer science programs. They point out that the number of large projects in industry demand this and suggest that the proof of the success of these accredited computer science programs should be seen in the reduction of failure in the design and operation of large computer programs. Software engineering programs can be thought of as a replacement for the old apprenticeship programs which taught the trades to workman (Stroulia, Bauer, Craig, Reid, & Wilson, 2011). The issue, however, is how to bring this effect into the classroom. Many educators feel that current practices of teaching engineering are not adequately preparing students for the real world of development. Nurkkala & Brandle (2011) summarize the problems with current teaching approaches: * No product--students are creating projects, not commercial grade products * Short duration--single semester, or two-semester, courses impose an artificial time constraint * High turnover--new students each semester means the talent pool remains shallow and student skills are not developing based on previous experience * Low complexity--by necessity given time constraints and skill sets * No maintenance--as a result of short duration, students do not experience a key aspect of development, the maintenance phase * No customer--most engineering projects do not interface with a real customer To address these shortcomings, different approaches to teaching engineering have emerged and been proposed in the literature. …

Lifelong learning is an important part in the career of an engineer in computer sciences. In this paper the characteristics of life long learning in Computer Sciences are worked out. In 2007 the European Commission launched a lifelong learning programme to enables people at all stages of their lives to take part in stimulating learning experiences. A network of seven European universities started within this programme a project designing a Master program in Computer Science that appeals to non-traditional students who may wish to study on a part-time and/or intermittent basis, in an international framework. (EMaCS means European Master Program in Computer Science) This paper describes how the EMaCS project approaches to the life long learning problems in Computer Science.

Structural genomics provides an important approach for characterizing and understanding systems biology. As a step toward better integrating protein three-dimensional (3D) structural information in cancer systems biology, we have constructed a Human Cancer Pathway Protein Interaction Network (HCPIN) by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions. Many well known cancer-associated proteins play central roles as "hubs" or "bottlenecks" in the HCPIN. At least half of HCPIN proteins are either directly associated with or interact with multiple signaling pathways. Although some 45% of residues in these proteins are in sequence segments that meet criteria sufficient for approximate homology modeling (Basic Local Alignment Search Tool (BLAST) E-value <10(-6)), only approximately 20% of residues in these proteins are structurally covered using high accuracy homology modeling criteria (i.e. BLAST E-value <10(-6) and at least 80% sequence identity) or by actual experimental structures. The HCPIN Website provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research. To complement and enrich cancer systems biology, the Northeast Structural Genomics Consortium is targeting >1000 human proteins and protein domains from the HCPIN for sample production and 3D structure determination. The long range goal of this effort is to provide a comprehensive 3D structure-function database for human cancer-associated proteins and protein complexes in the context of their interaction networks. The network-based target selection (BioNet) approach described here is an example of a general strategy for targeting co-functioning proteins by structural genomics projects.

Engaging and maintaining student engagement with the content of a course in formal language theory and the theory of computation is notoriously difficult. A major factor is student's perception of the relevance of the required mathematical material to computer science as they have studied the discipline. Usually, the mathematical material discourages students and for many it forms an insurmountable barrier. This paper describes the construction of a course using the discovery learning technique known as the Moore Method that directly addresses student engagement with this material. The results of the delivery of this course were that students remained engaged with the course throughout the semester and enthusiastically received the pedagogical approach employed. While the course described was delivered to a small class in a liberal arts college, it may be adapted to larger class sizes and taught in any computer science program.

Providing stimulating and real-life experiences is a key component in teaching software project management in Computer Science or Software Engineering programs. The diversity of topics that need to be addressed and restrictions that should be considered in university courses make a challenging task of it. This paper presents a serious game, called “White Crow PM” whose objective is to make students aware of the risks they might face during software development projects. The paper describes the game design steps and provides results of its validation in Computer Science programs in two Mexican universities. The collected data showed that the participants had fun playing the game and its content is relevant for software project management courses. Although the game needs to be validated in other settings with more participants, we conclude that it fulfills the goal of motivating discussion and increasing awareness of project management concerns among students.

This study investigated whether student academic achievement in college computer science programs in Taiwan could be predicted by factors reported to be effective in U.S. studies. Subjects were 940 college students enrolled in five universities offering computer science programs. A correlation study was conducted and prediction models were established. The predictive powers of college entrance examination (CEE) scores in relation to subsequent college performance appeared to be limited. Overall high school achievement and math course averages were identified as effective performance predictors. The close relationship between performance in introductory computer science courses and performance in complete computer science programs was validated. Significant linear prediction models with limited predictive powers were generated for overall performance but not for introductory computer science course performance. Model predictive powers were significantly improved when performance in introductory computer science courses was included in the models. No significant gender differences were found for CEE performance. However, female subjects outperformed male counterparts in course performance at both the high school and college levels.

Computational Biology

As a female computer science educator, I've watched with growing alarm the drop in enrollment in our Computer Science programs from a ratio of 1:1 of males and females in 1983, to a current ratio of 5:1. The lack of interest of female students in Computer Science is still a very serious problem. As educators we should all be watching our own campus and addressing this problem. The panelists assembled from various institutions will address the issues of gender imbalance and relate their experiences in implementing solutions to counter this problem. Two of the panelist will discuss utilization of the World Wide Web addressing reasons for creating both Web sites. As long as this gender imbalance exists in our schools we need to continue our dialog to share and develop new ideas to encourage female participation in Computer Science Programs. The audience will be welcomed to participate in a larger group discussion.

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Background Despite ongoing calls for prioritizing K-12 computer science (CS) education, an enduring gender gap exists. Objective We explored one high school CS program where female participation was consistently higher than state averages to better understand how the program was developed. Method Using a case study method, data were collected over three-months through interviews, observations, course documents, student reflections, and researcher reflections. Constant comparative analysis was employed to analyze data throughout and following data generation. Findings Recruitment and teacher support were key practices. Recruitment practices included letter writing campaigns and recruiting from introductory CS courses. Teacher support came from counselors, administrators, and other teachers. While the CS program was consistently more gender-inclusive, the focus when building the program had been on supporting all students, not only female students. Implications Recruitment should be active and purposeful, but using academic indicators for targeted recruitment campaigns can limit student exposure. Teachers need support for broadening participation, particularly from counselors and administrators, who must also be aware of what CS is and their role in these efforts. Opportunities for coteaching within CS programs can be beneficial for growth. Overall, broadening participation must be a holistic effort, supported by school-wide stakeholders, not only CS teachers.

The Department of Computer Science at the University of Southern California recently created two new degree programs, namely a Bachelor's Program in Computer Science (Games) and a Master's Program in Computer Science (Game Development). In this paper, we discuss two projects that use games as motivator. First, the Computer Games in the Classroom Project develops stand-alone projects on standard artificial intelligence topics that use video-game technology to motivate the students but do not require the students to use game engines. Second, the Pinball Project develops the necessary hardware and software to enable students to learn concepts from robotics by developing games on actual pinball machines.&#x0D;

Computer Science and Systems Biology have heralded remarkable technological advances in understanding the complex biological systems including human biochemical, molecular and neural pathways and networks. Systems biology integrates the computer applications and experimental biology in modeling’s, predictions and characterizations of complex and dynamic properties of biological systems. Particularly, multi-omics studies, high-throughput sequencing techniques and microarray techniques made possible the generation of large datasets from biological systems that could help in understanding the comprehensive molecular pathways, systems functions and behaviors. In the last decade, the computer science and systems biology approaches increased the interest in pathway based biomarker identification, identifying disease genes and drug targets, generation of global genetic interaction maps, and development of new diagnosis and therapeutics methods for deadly diseases and contemporary outbreaks. In this letter, I summarize the breakthroughs of the decade and future challenges in uncover the complex components of biological systems.

In today's technological market, job candidates must possess technical and communication skills to acquire a desired position. Computer science programs, for the most part, provide the technological training, but are inconsistent in teaching students all the necessary communication skills. In many computer science curricula faculty members realizing the importance of improving writing ability have incorporated writing intensive courses. However, many computer science curricula neglect oral communication, largely because of the amount of class time needed to make presentations. Several gaps exist between computer science curricula and business world reality. Computer science curricula must teach students to listen and express themselves clearly, since getting the maximum utilization of an information resource requires contact with the user community. This is not to say that educators have ignored industry requests. The emerging trend in computer science curricula is to stress written and oral communication skills. This article discusses the importance of incorporating speaking intensive courses into computer science programs. In addition, this article reviews two courses that have included speeches and presentations. Finally it presents a new way to grade oral communication.

At this time, along with the development of the times, technology has also developed very rapidly, especially in the field of computers. Where can we know that the development of this technology can help human work. In the world of education, computer science is very necessary so that teachers or students do not lag behind in the development of today's times. For this reason, training in computer science is needed. Many of us know computers only limited to Ms. Office alone because it is often used in everyday life, but actually in computer science there are many applications/programs that can help human work to be easier. For this reason, this training was made to introduce one of the application programs in computer science, namely the application of visual studio 2010 and SQL server 2008. Where this application can create programs according to our wishes to help make our work easier. The object that will be used as the location of service is the teachers at the Al JABAR Middle School. In this service, the team wants to do it in the form of training and talk shows about Simple Design Training Using Visual Studio 2010 and SQL Server 2008 Applications at IT AL JABAR Junior High School. The results obtained at the IT Al-Jabar Junior High School from this activity are that teachers can increase their knowledge in computer science, especially in making simple designs using Visual Studio 2010 and SQL Server 2008 applications which are useful for teaching materials to their students