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Course Criteria
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5.00 Credits
Perl, the Practical Extraction and Report Language, was conceived, created, and continuously developed as a text processing language for Unix-like(Linux and Unix) operating systems. Most of its semantics and syntax is tied directly to other Linux/Unix based languages such as C, awk, sh and Unix power utilities like grep and sed. Some of its power also derives from native Linux and Unix process control and file system operations. This course covers the core Perl language in a Linux and Unix based instruction environment to prepare the student for significant Perl programming challenges in the "real" world, as well as further study in intermediate and advanced Perl programming courses. Advisory: CIS 68A and one or more of CIS 15A or 25A or 27A; or equivalent experience. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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5.00 Credits
This course will introduce BioPerl modules in the analysis of bioinformatics data, including downloading, installing and configuring BioPerl in a Windows environment. Using BioPerl modules, this course will show the student how to retrieve, analyze and manipulate genomic/proteomics sequences from databases such as GenBank and GenPept, RefSeq, SWISSPROT, EMBL, etc. It will show how to use BioPerl modules to convert between and from various file formats including FASTA, SWISSPROT, and EMBL. It includes extracting annotations/features from sequence files, performing similar sequence searches and using sequence alignments. BioPerl modules exercises include running applications such as BLAST, Smith-Waterman, Clustalw, HMMER etc. This course is intended for bioinformatics students with a strong foundation in Perl, which is provided by the course CIS 68J. Advisory: CIS 68E or COIN 68 or equivalent. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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5.00 Credits
Provides a strong foundation in Perl programming for Bioinformatics, which has become a required 'lab skill' for biologists. It shows the student how to use Perl in a Windows environment to solve programming problems such as creating, modifying, comparing and deleting biological data files, searching for motifs in these data files, manipulating sequences found in these data files etc. Elucidates basic programming concepts such as operators, conditional and looping constructs, file operations and regular expressions. Class exercises emphasize use of biological sequence data for bioinformatics problem solving. This course provides the requisite skills to successfully complete the CIS 68H course. Advisory: CIS 50A or equivalent. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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5.00 Credits
This course will introduce students to the Python language and environment. Python is a portable, interpreted, object-oriented programming language that is often compared to Perl, Java, Scheme and Tcl. The language has an elegant syntax, dynamic typing, and a small number of powerful, high-level data types. It also has modules, classes, and exceptions. The modules provide interfaces to many system calls and libraries, as well as to various windowing systems(X11, Motif, Tk, Mac, MFC). New built-in modules are easily written in C or C++. Such extension modules can define new functions and variables as well as new object types. Advisory: CIS 15A or 27A, and CIS 68A. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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5.00 Credits
Extends the students' understanding of how to write effective applications in the Python programming language. Covers topics that allow a Python program to interface to users, networked applications and databases. Includes advanced topics like multithreading and regular expressions. Enforces object oriented design, thorough documentation, testing and conventional programming style. Advisory: CIS 68K. Four hours lecture, four hours laboratory GE Area: Non-GE Applicable
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5.00 Credits
This course presents core Perl language features used to manage the development and complexity of Perl programs requiring hundreds if not thousands of lines of code. An in depth presentation of references and arbitrarily complex data structures provide a basis for object-oriented Perl. Perl and Linux/Unix based mechanisms for release cycle control, unit testing, and code packaging (i.e. a distribution) are also presented. This course is intended to leverage the environment of the Linux/UNIX operating systems and it's various subsystems (i.e. filesystems, process management, memory management, etc.) and therefore requires a working knowledge on the part of the student and a substantial background on the part of the instructor. Advisories: CIS 68E or some Perl programming experience; CIS 68B. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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5.00 Credits
A language-independent study of current software development methodologies. The stages of systems analysis, product design, implementation and testing are practiced. Collaborative, interactive design and technical writing are problem solving techniques learned. Advisory: Any structured programming class. Four hours lecture, four hours laboratory. GE Area: Non-GE Applicable
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3.00 Credits
Off-campus supervised experiential education of CIS students in database administration, computer software development or Informatics. Opportunity for practical application of knowledge, skills and abilities acquired in CIS and related course work. Exposure to varied protocols, methodologies and practices in a professional working environment. Repeatability: May be taken for a maximum of 18 units of credit. Nine hours laboratory. GE Area: Non-GE Applicable
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4.00 Credits
Off-campus supervised experiential education of CIS students in database administration, computer software development or Informatics. Opportunity for practical application of knowledge, skills and abilities acquired in CIS and related course work. Exposure to varied protocols, methodologies and practices in a professional working environment. 12 hours laboratory. GE Area: Non-GE Applicable
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6.00 Credits
Off-campus supervised experiential education of CIS students in database administration, computer software development or Informatics. Opportunity for practical application of knowledge, skills and abilities acquired in CIS and related course work. Exposure to varied protocols, methodologies and practices in a professional working environment. 18 hours laboratory. GE Area: Non-GE Applicable
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