Developing and Implementing a Combined Chemistry and Informatics

Article pubs.acs.org/jchemeduc

Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic Jiří Jirát,†,‡ Petr Č ech,†,‡ Jiří Znamenácě k,†,‡ Miroslav Šimek,‡ Ctibor Škuta,† Tomás ̌ Vaněk,§ Eva Dibuszová,‡ Miloslav Nič,† and Daniel Svozil*,† †

Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, ‡Center for Information Services, and §Institute of Chemical Engineering, Faculty of Chemical Engineering, Institute of Chemical Technology, Technická 5, CZ-166 28, Prague, Czech Republic ABSTRACT: Experience developing multidisciplinary bachelor’s and master’s curricula involving intertwined chemistry, informatics, and librarianship− editorship skills is described. The bachelor’s curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chemical Technology Prague: a sole publisher of chemical literature in Czech Republic), with the aim to educate a new generation of information retrieval and e-publishing professionals in the science−technology− medicine (STM) field. This cooperation together with a set of specifically tailored courses gave students the insights into real-world issues of STM publishing. The master’s curriculum, heavily relying on the bachelor’s stage, inclines towards cheminformatics and deepens software engineering skills. Successes, pitfalls, and failures are described, together with proposed changes and future directions. KEYWORDS: First-Year Undergraduate/General, Second-Year Undergraduate, Upper-Division Undergraduate, Graduate Education/Research, Interdisciplinary/Multidisciplinary, Chemoinformatics, Curriculum

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informatics, and librarianship−editorship skills to produce specialists educated in storing and using databases of chemical and related biological information; in handling chemical information on the Web and in the scholarly literature; and in modern e-publishing in the science−technology−medicine (STM) area.6 Institute of Chemical Technology, Prague (ICT Prague) is a public university that consists of four faculties, Faculty of Chemical Technology, Faculty of Environmental Technology, Faculty of Food and Biochemical Technology, and Faculty of Chemical Engineering. Its study programs and research cover almost all branches of chemistry, chemical engineering, food chemistry and technology, biochemistry, refining, water-treatment, power and biological sciences and technologies, as well as environment protection, materials sciences and other chemistry-based fields of study.7 Apart from individual faculties, ICT Prague’s organizational structure includes not only a Central Library, but also its own publishing house (ICT Prague Press).8 The tasks of ICT Prague Press are focused on in-house production of printed textbooks and supporting materials for ICT Prague. ICT Press remains virtually the sole publisher of chemical literature in the Czech Republic and is facing diminishing numbers of educated technical editors and science editors. At the same time fast technology changes in the publishing technology and users’ demand for e-books9 require a new style of book and publication preparation. High demand

hemists have always produced vast amounts of information, which is challenging to store and search mainly due to the special language of chemistry focusing on chemical structures and reactions. The field of chemical information has a long history, starting with publishing of printed journals and patents and followed by the development of printed secondary chemical information systems. The latest developments in the field of chemical information include an availability of full-text electronic journals, Web interfaces for chemical information applications, and an enhanced structure and reaction indexing and searching. For many years, the field of chemical information handling was closely related to the drug discovery applications, and the pharmaceutical industry became a strong supporter of the field. Recently, the technological innovations in combinatorial synthesis, highthroughput screening (HTS), X-ray crystallography, and NMR spectroscopy resulted in a vast increase in the amount of chemical information available. With the advent of chemical biology and academic screening programs,1 the growing opensource movement,2 and government sponsorship of key databases such as Pubchem3 led to the broadening of the chemical informatics’ scope, and ultimately a new field “cheminformatics” (sometimes also spelled as “chemoinformatics”) emerged.4 The ever-increasing need for techniques that allow the data to be stored, aggregated, and manipulated is followed by growing demand for people trained and experienced in these methods.5 We describe an attempt to create a contemporary multidisciplinary specialization that combines chemistry, © 2013 American Chemical Society and Division of Chemical Education, Inc.

Published: January 22, 2013 315

dx.doi.org/10.1021/ed3001446 | J. Chem. Educ. 2013, 90, 315−319

Journal of Chemical Education

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for interactive Web-based publications requires Web developers rather than desktop publishing specialists. The ICT Central Library is the largest and best-equipped chemistry and chemical engineering library in Czech Republic, offering a comprehensive collection of specialized chemical literature that includes reference information sources and journals. It is focused on providing primary and secondary electronic sources that are accessible in the whole ICT network. The library relies on a strong mutually cooperative relationship between the library staff and university teachers that represents a proven and successful approach in chemical information education.10 However, with the massive advent of electronic online information sources for chemistry, educational programs to train librarians by the Faculties of Arts at Czech universities has become insufficient to cover all aspects needed for technically oriented libraries. In cooperation with the ICT Prague Press and the ICT Central Library, a new specialization called “Informatics and Chemistry” was developed under the bachelor program “Applied Chemistry and Materials”. This specialization opened for admission after two years of preparation in 2004. The ICT Press and ICT Library became official partners, participating with teaching and projects. Three years later in 2007, master’s program “Applied Informatics in Chemistry” was also established.

Table 1. Bachelor’s Curriculum Semester

Mandatory Coursesa

1

Chemical Calculations General and Inorganic Chemistry I Internet Publishingb Operating Systems and Networksb Mathematics I Inorganic Chemistry: Laboratory I Organic Chemistry I Fundamentals of Ecology XML Technologiesa Project Ib Physics I Organic Chemistry: Laboratory I Transformation and Processing of XML Documentsb Physics II Project IIb Biochemistry I Physical Chemistry I Scripting Programming Languages Ib Analytical Chemistry I Unit Operations of Chemical Engineering I Applied Statistics Toxicology Scripting Programming Languages IIb Chemical Informatics Project IIIb Bachelor’s Thesis

2

3

4

5

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CURRICULUM DEVELOPMENTS The new bachelor and master levels are described. A bachelor’s study program takes three years and must be completed in due form with a final state examination that includes a defense of a bachelor thesis. Graduates of bachelor study programs are awarded the academic degree “bachelor”, abbreviated as “Bc.”, used in front of the name. Bc. is comparable to an undergraduate academic degree BSc. A master’s study is a follow up to a bachelor’s study program. The standard length of such a study is two years, and it is complemented by a final state examination and a defense of a diploma thesis. Graduates of master study programs at the Czech technical universities are awarded the “Engineer” (abbreviated as “Ing.”) academic degree. The education in most Czech universities is Bolognacompliant11 meaning that a usual 5-year degree is split into an initial 3-year (bachelor’s) degree and a subsequent 2-years (master’s) degree. The general idea of the Bologna declaration is that these two stages are relatively independent allowing a smooth transition between study subjects or universities. When creating the original version of the curriculum, students who had good math and chemistry knowledge, good computer and programming skills, and proper foreign language and native language skills were targeted. The bachelor’s curriculum consists of two interlinked axes that are taught in parallel: (i) chemistry and engineering and (ii) informatics with an emphasis on Web and publishing. The contents of the “chemistry and engineering” axis were predominantly dictated by the university and faculty rules. The informatics courses were proposed as advanced courses built on a relatively good foundation of basic knowledge in computer science. A detailed curriculum is listed in Table 1. The master’s curriculum was set up as a multidisciplinary combination of computer science and natural sciences and technology, and contains subjects such as computational chemistry, chemoinformatics and bioinformatics, multivariate statistical analysis, and data mining. In addition, software engineering skills are strengthened by covering database and

6 a

Only the major courses listed. bInformatics axis.

software architecture (Java programming language). A detailed curriculum is listed in Table 2. The courses “Introduction to Table 2. Master’s Curriculum Semester

Course

1

Introduction to Software Architecture Statistical Data Analysis Databases Fundamentals of Molecular Genetics Laboratory Project I Theoretical and Computational Chemistry Laboratory Project II Advanced Chemical Informatics Software Architecture Data Mining Knowledge Modeling Excursions Specialized Practice Computations and Visualization of Molecules Computer Aided Chemical Structure Processing Laboratory Project III Essential Bioinformatics Web Applications in Python Diploma Thesis

2

3

4

Software Architecture” and “Databases” followed by the “Software Architecture” supply all necessary skills and knowledge from the software engineering for subsequent multidisciplinary courses. By completing these courses, students gain the knowledge of programming in the Java and SQL languages and in a database design. Also the ensuing multidisciplinary 316



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courses are interconnected: “Statistical Data Analysis” represents a necessary prerequisite for a “Data Mining” course, “Essential Bioinformatics” builds on “Fundamentals of Molecular Genetics” and “Data Mining”, and “Theoretical and Computational Chemistry” followed by “Computations and Visualization of Molecules” enriches the education in informatics applied to natural sciences. “Computer Aided Chemical Structure Processing” combines software engineering skills, builds on “Advanced Chemical Informatics” and is coupled with “Web Applications in Python”.

seeking, programming, chemical informatics, and corresponding knowledge of chemistry and chemical engineering. Three projects (one for each semester) at the master’s level are focused on the interdisciplinary usage of skills, and subjects such as chemoinformatics or bioinformatics are practiced. Bachelor Projects

Project I (1st year) is bound to the “Fundamentals of Ecology” course and is simple and introductory: locating journal articles with an ecology focus for all main topics covered during the course, writing abstracts and citations in simple XML format. Project II (2nd year) builds on courses in “Internet Publishing”, “XML Technologies”, “General and Inorganic Chemistry”, and “Organic Chemistry”. Its aim is to encode small subset of substances (usually defined as substances in one term in Ullman’s encyclopedia, e.g., Pyrazolone Derivatives, Xylenes, Antioxidants, Artificial Sweeteners, etc.) in XML format. This includes proposing a data structure (including CAS RN, InChI, SMILES, structure formula in SVG, etc.) and writing appropriate formal grammar in DTD, XML Schema, and Relax NG schema. The last step is transforming the content to a Web site using XSLT (eXtensible Stylesheet Transformations) and creating various indexes: compound name index, summary formula index, CAS RN index, structure index, and so forth plus detailed descriptions for each compound. Project III (3rd year), which is required by the Chemical Engineering department, comprises a complex library research, collecting facts for a more-or-less real-world chemical engineering project, from general information, gray literature (white papers, business catalogs), to traditional scientific publications. This project is tied to the course “Unit Operations of Chemical Engineering I”.

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INFORMATICS AXIS Computer Science courses are focused on Web applications development. During bachelor’s study, students gain sufficient basic informatics skills to be able to start working in the Web development area or to advance to the master’s study. The key parts of the bachelor’s study are scripting languages and Web technologies (HTML, XML technologies). At the master’s level students learn standard software development techniques and apply these to the development of scientific applications related to the chemoinformatics or bioinformatics. The choice of lectured programming languages was set to two platform-independent programming languages. Python12 was selected as an optimal programming language suitable both for beginners and advanced users, easy to learn, and at the same time powerful, with a large collection of libraries that also offers a wide range of accessible chemical and bioinformatics toolkits. Java programming language13 is introduced during master’s study, giving students the opportunity to gain substantial skills in an industry-wide adopted standard. In the last semester of the master’s program, in the course Computer Aided Chemical Structure Processing, students have to use both programming languages, implementing their own routines, and utilizing available open-source or commercial chemoinformatics libraries (OpenBabel,2e Pybel,14 CDK,2a Marvin,15 etc.).

Masters Projects

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Project I represents a deep literature search for given topic, with a written report of the primary resources identified in the search. Selected topics are intentionally selected outside students’ interests to force them to dive into unknown topic. The project ends with a public 10 min presentation in the English language, which requires students to thoroughly consider what points are important and how to emphasize them. Project II emphasizes programming skills and team-skills. Students develop a software application in a team, starting from “customer requirements” and mock-ups, and ending with a fullfledged application along with documentation. This project builds on the courses “Introduction to Software Architecture”, “Software Architecture” and “Databases”. The team uses the Scrum process16 to create complex software in a three month period. One teacher has the role of Product Owner (“customer”, defines requirements) and the other one is Scrum Master (guides the team). One example of a project is the development of a complex graphical user interface (GUI) with XMR software that is used for dynamic simulations of catalytic monolithic reactors.17 This GUI is developed in collaboration with the Department of Chemical Engineering. A second example is a CzeChem, a database of organic compounds synthesized in Czech Republic. This type of project usually involves a partner from an external organization. Project III is usually tightly bound to a Diploma Thesis topic combining both library research and programming and work.

CHEMISTRY AXIS For many years, the core of all study academic programs at the ICT Prague was fixed for first three years (six semesters) and shared among all faculties as a “common base”. Before the division to two-stage degrees (Bologna-compliant11), the “common base” consisted of nearly all courses listed in Table 1 without a footnote b, with a mandatory duration of twosemesters: Mathematics I + II, Physics I + II + labs, General and Inorganic Chemistry I + II + labs, Organic Chemistry I + II + labs, Physical Chemistry I + II + labs, Unit Operations of Chemical Engineering I + II + labs, Analytical Chemistry I + II + labs, Biochemistry I + II, Toxicology, Applied Statistics + minor courses. Although minor variations existed (e.g., Chemical Engineering faculty did not include Biochemistry II), it remained practically unified until the change to a twodegree program. Subsequently, the “common base” was relaxed and is now reduced to mandatory one-semester versions (i.e., Mathematics I, Physics I, etc.), and faculties define lists of other mandatory courses (the II-versions and specialization courses) for each study program separately.

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PROJECTS, EXCURSION, AND SPECIALIZED PRACTICE Hands-on experience is critical for informatics skills. The number of projects at the bachelor’s level is three (one each year). All projects are focused on a combination of information 317



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mandatory courses “Librarianship” and “Editorial Processes” (not shown in Table 1) were suppressed and abandoned, reflecting the overall trend: a shift from editor−librarian specialist to chemist−application developer. The following external factors also contributed to the problems mentioned above: drastic deterioration of skills for Czech students after primary school in reading literacy, mathematics, and science between years 2000 and 2009 reported by the PISA program (OECD Program for International Student Assessment). Czech students had the worst decline in mathematics and science, and a severe decline in a reading literacy.18 In addition, there was a rapid increase in the number of higher-education institutions in Czech Republic that compete for students:19 there were 23 in 1989 and 62 in 2004. Finally, science and technology studies, as somewhat difficult disciplines, are not the first choice for a vast majority of students and a significant decrease in the total number of pupils in primary and secondary schools in the Czech Republic19 resulted is fewer students interested in this area. The success rate for finishing bachelor’s degree has been about 30% with almost all students continuing with master’s study, where the failure rate is much lower. The failures during the master’s study were usually caused by insufficient computer skills. Only a few students were attracted to the master’s degree after earning bachelor’s degree in another chemistry program. However, such students belonged to a superior group as they passed chemistry bachelor’s program and were able to fill the gap in informatics−computer science. In 2012, the total number of students in both bachelor’s and master’s program was about 30. Out of 20 students who successfully finished the master’s study since 2009, five decided to continue with Ph.D. studies. All students who earned bachelors and master’s degrees (in “Informatics and Chemistry” and in “Applied Informatics and Chemistry”) clearly proved that such combination is useful and required. Their jobs include information broker (chemical or pharmaceutical information), developers of applications related to REACH (e.g., predictions of toxicological properties), Web content developers, Webmasters, and chemical laboratory heads.

Masters Excursions and Specialized Practice

The course “Excursions” is common for all study programs and consists of several one-day on-site visits to selected industrial or research organizations. The selection for students of the informatics and chemistry combination usually includes several organizations from the organic chemistry and pharmaceutical sector and one or two specialized information centers or libraries. Specialized Practice is at least a three-week-long regular job, has to be outside the university and has to be related to students’ study orientation. Students have the option to find their own preferred placement or they select it from those proposed by partner organizations and organized by university.

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EXPECTATIONS AND FINDINGS The creation of the two-stage Bologna-compliant11 degrees in 2002−2003 caused considerable changes in the traditional curricula allowing the formation of new specializations (e.g., such as our “Informatics and Chemistry”) and the relaxation of stringent rules in existing ones. However, the split into the bachelor and master levels was problematic when creating interdisciplinary courses. Therefore, we decided to build the bachelor’s degree utilizing two parallel and rather independent “axes” (informatics and chemistry), which were interconnected by projects. The design that combines two axes in parallel proved to be reasonable and viable; however, to absorb all knowledge and acquire all skills thoroughly in both areas (general chemistry− engineering curriculum and IT) requires substantial time. The opposite possibility, to complete the chemistry stage first and continue with computer science courses, would disrupt consecutive courses, cause serious organizational complications, and result in a lost opportunity to easily combine informatics and chemistry−engineering in projects. In the first three years after initiating the process of consolidation of study programs, the aim was to have study programs manageable from an organizational point of view, to maintain certain levels of quality, and to ensure a smooth transition to compatible masters’ levels for most of the students. However, faculty policy has changed and now requires an increase in the compatibility of specialization “Informatics and Chemistry” curriculum with the bachelor program “Applied Chemistry and Materials”. In the first stage, new mandatory courses and laboratories were added, but this resulted in an overcrowded curriculum and even the best students struggled to fulfill all requirements properly in time. Finally, the proportion of informatics courses was reduced resulting in a ratio 70:30 for general curriculum relative to the informatics axis. Another serious and underestimated problem was the absence of defined levels of informatics skills in secondary schools. Thus, students leaving secondary education differ significantly in their computer skills. These differences were enhanced by the interdisciplinary nature of “Informatics and Chemistry”: in the first year one could expect students excellent in chemistry and math, but moderate in computer skills; excellent programmers who fail in chemistry; sometimes students excellent in all of the courses; and most often, students with moderate skills in all disciplines. And, as the last disillusionment, the triple combination of humanities (librarianship, editorship), chemistry, and informatics was simply unrealistic. As a result, the bachelor’s

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FUTURE DIRECTIONS After eight years, the concept of specialization was reassessed and its broad scope was reduced. The chemical axis remains stable and nearly intact. However, the informatics axis was revised to closely follow modern trends in software engineering and computer science areas. The following changes have been proposed and will be introduced. During bachelor’s studies, students will attend courses on “Algorithm Development”, “Databases”, and “Programming”. Courses on XML technologies will be moved to the master’s program. Web development lectures will be based on modern techniques including HTML5, JavaScript, and PHP20 languages. To increase the attractiveness of the graduates for employers from industry or ICT companies, the Python programming language will be substituted by C# language in the bachelor’s program. These changes also reflect the needs of our graduates when looking for jobs in informatics related areas.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. 318



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Notes

research: A curriculum model that works. J. Chem. Educ. 2009, 86 (8), 940. (11) Bologna Process. http://ec.europa.eu/education/highereducation/doc1290_en.htm (accessed Jan 2013). (12) Python programming language. http://www.python.org/ (accessed Jan 2013). (13) Java programming language. http://www.oracle.com/ technetwork/java/index.html (accessed Jan 2013). (14) O’Boyle, N.; Morley, C.; Hutchison, G. Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit. Chem. Cent. J. 2008, 2 (1), 5. (15) Marvin. http://www.chemaxon.com (accessed Jan 2013). (16) Scrum. http://www.scrum.org/ (accessed Jan 2013). (17) Jirat, J.; Kubicek, M.; Marek, M. A CAPE tool for evaluation of adsorber-reactor systems for treatment of exhausts from mobile sources. Comput. Chem. Eng. 2001, 25 (4−6), 643−651. (18) OECD PISA 2009 Database, tables v.2.1, v.2.2, v.2.4 and v.4.3. http://dx.doi.org/10.1787/888932359948 (accessed Jan 2013) (19) Centre for Higher Education Studies. Tertiary Education in the Czech RepublicCountry Background Report for OECD Thematic Review of Tertiary Education; Ministry of Education, Youth and Sports Czech Republic: Prague, 2006. (20) PHP: Hypertext Preprocessor. http://www.php.net/ (accessed Jan 2013).

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by the Ministry of Education of the Czech Republic MSM6046137302.

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Developing and Implementing a Combined Chemistry and Informatics

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