Introduction to Linux, basic commands, working with files, file attributes, installing programs using rpm, working with basic editors sed, awk and vi, using the shell, pipes, wildcards, checking processes, killing processes, basic decision making statements: if...then.... else...if - test - while...do...done - until...do...done - for...in..Do...done - case...in...esac - select...in...do., basic regular expressions, using grep command, string search applications using regular expressions. Structured and unstructured data, XML fundamentals, XML documents and XML files, elements and character tags, attributes, XML names, CDATA sections, XML declarations, DTD, element declarations, attribute declarations, namespaces, programming applications of XML; General features of NCBI’s Molecular biology data model, BioXML, NeuroML, Chemical Markup Languages (CML), Microarray ML(MAML), RiboML and SBML.
Internet Addresses, Internet Protocol, Transport layer, Upper layer protocols, Internet access and applications. Overview of HTML and HTTP; Web servers, Web access, Security, WWW (World Wide Web) proxies, HTML applications related to biotechnology. Novell’s WWW service, Web based applications, Biology search engines, legal and ethical issues. Introduction to flat files, DBMS and RDBMS, E-R relationship, Introduction to SQL, basic commands, using SQL in MS Access, creating and modifying tables, joining tables, simple queries using SQL, inner join, outer joins.
Overview of ontologies, gene ontologies, Open biological ontologies (OBO) and its applications, TAMBIS ontology, cell cycle ontology, GeneX ontology. Building ontology, ontology development tools (protégé 2000, GKB editor, OilEd), Ontology integration of bioontologies. Different types of data formats (CSV and tabbed formats for general file representation, data cleaning, flat file) Introduction to MATLAB, features of MATLAB toolbox, Usage of MATLAB towards bio statistical and biochemical applications. Modeling of biochemical and biotechnological systems using MATLAB scientific computing environment.
Overview of C programming concepts, Variables, Operators, Statements, Functions and Pointers. Introduction to Classes, Objects, C++ string classes, Introduction to OOPs concepts with respect to C++ (Encapsulation, polymorphism, Inheritance, Abstraction, Dynamic binding), data types, Arrays. Introduction to basic concepts of Bioperl.
Writing a C program using numerical analysis technique towards solving the differential equations to biotechnology (such as finding the thermal death kinetics of microorganisms, holding time for sterilization, estimating the length of the lag phase, calculation of specific growth rate, doubling time, and substrate-to-cell yield coefficient, etc.). Write a C++ Program to find the optimum pH and temperature for maximum enzyme activity, to derive the column height needed to achieve the specified degree of conversion in a fluidized-bed biofilm reactor, to find the optimal dilution rate for maximum cell productivity, etc. Usage of NCBI’s C++ tool kit to demonstrate certain features of sequence analysis.