Chemical Informatics - MC270P10
Title: Chemická informatika
Guaranteed by: Department of Organic Chemistry (31-270)
Faculty: Faculty of Science
Actual: from 2024
Semester: summer
E-Credits: 3
Examination process: summer s.:
Hours per week, examination: summer s.:1/1, C [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Additional information: http://dl2.cuni.cz/course/view.php?id=1413
Note: enabled for web enrollment
priority enrollment if the course is part of the study plan
Guarantor: doc. RNDr. Jindřich Jindřich, CSc.
Teacher(s): doc. RNDr. Jindřich Jindřich, CSc.
Incompatibility : MC200P01, MC230P22
Is incompatible with: MC270P10M, MC200P01, MC230P22
Is interchangeable with: MC270P10M
Opinion survey results   Examination dates   SS schedule    E-learning course
Annotation -
Communication in chemistry: molecular visualization tools and Internet sites; chemistry newsgroups and discussion lists; science writing aids (software); the publication process - primary, secondary, and tertiary sources. How and where to start: guides to chemical information sources and databases; general information on computer searching; current awareness, reviews, and document delivery; background reading: dictionaries, encyclopedias, and other books; introduction to Chemical Abstracts (SciFinder), Beilstein (Reaxys), Web of Science.
Last update: Jindřich Jindřich, doc. RNDr., CSc. (08.05.2012)
Literature -

All materials needed to complete the course are available at http://dl2.cuni.cz/course/view.php?id=1413 for the students signed for the course.

Last update: Jindřich Jindřich, doc. RNDr., CSc. (01.06.2018)
Requirements to the exam -

To complete the course, a student has to fulfill the following:

- sign into the online course on dl2.cuni.cz

- solve in time an assignment for every lecture (once a week) to at least 60 %

- solve the final online test, to at least 60 %

Last update: Jindřich Jindřich, doc. RNDr., CSc. (01.06.2018)
Syllabus -

1. Visualization using HTML, basics of HTML, data file formats, web browsers and plugins. E-mail discussion groups.

2. Tools to create scientific documents - Overview of software used for the creation of scientific publications. Publication process - definition of terms primary, secondary and tertiary literature, bibliographic databases.

3. Guides to chemical resources (Database summary sheets, search servers). Computer searching (search servers, relational databases, basics of SQL).

4. Current awareness, e-mail alerts, online journals, bibliographic databases (Web of Science), documents delivery. Dictionaries, encyclopedia, tables.

5. SciFinder. How to use software to access CAS databases - CA Plus, Registry, ...

6. Reaxys - basics of compounds search. 

7. Zotero - personal bibliographics database.

8. Patents. Definition, conditions for assignment, protection of rights, patent databases. Toxicological information. Safety data sheets (MSDS), toxicological databases (Toxnet, HSDB).

10. Command line - MS Windows. Basics of batch scripts.

11. How to prepare PowerPoint presentations. Organization of material for visual presentation, the layout of presentation.

12. Cambridge Structural Database.

13. Final online test.

Last update: Jindřich Jindřich, doc. RNDr., CSc. (01.06.2018)
Learning outcomes -

After completing the course, the student:

Creates a simple web page using HTML and knows its meaning and structure (basic tags and attributes and their functions).

Uses advanced functions of word processors (Microsoft Word, or Open Office Write) to create automatically numbered objects (figures, diagrams, tables), cross-reference them from text and create content.

Uses a chemical structure drawing program (ChemDraw, ChemSketch) to draw structures and schemes and ways to insert them into a word processor.

Searches the largest commercial chemical databases (SciFinder-n, Reaxys) for compounds according to their properties (m.p., b.p., ...), names or structures, and also searches for chemical reactions according to the structure of the starting substances or products.

Searches scientific publication databases (Web of Science, SciFinder-n, Reaxys) for publications by keywords, authors, publication type and other parameters using logical operators, field names and extension symbols.

He knows the basic meaning of patents and searches the largest patent databases for patents using advanced search techniques as well as patent-specific parameters.

Uses a personal bibliographic database (Zotero, possibly Mendeley) to collect bibliographic citations for the final thesis, knows how to annotate the citation records appropriately, and can use the database when writing the thesis.

Uses the command line to run operating system commands and creates a batch file to run multiple commands at once.

Looks up the 3D structures of molecules in a crystallographic database (CSD), which it connects to remotely using the command line, and uses them to create publication-quality images.

Last update: Jindřich Jindřich, doc. RNDr., CSc. (12.08.2024)