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OFFICIAL SCHEDULE (Revised 16 Dec 2009)
Saturday Software Classes - NCBI C Toolkit Basics Prerequisite: Introductory level C/C++/Java programming is assumed.
Unix command-line familiarity is assumed. VENUE S1A Computer Room, Level 4. 10-12am Saturdays To apply to this year or next year's Workshop contact Christopher Hogue RESOURCES Introduction to Linux Basics Linux Ownership and Permissions NCBI C Toolkit Cross Reference
NCBI C Toolkit Source Browser NCBI C Toolkit CVS Source Viewer NCBI C toolkit Documentation (Old…) ASN.1 Browser (NCBI and BIND Combined) Sat Oct 24 2009 Lecture 1. Introduction to C Compiling and Make. -C. Hogue Attached below: 091024_Introduction_to_C_compiling_and_Make.ppt Sat Oct 31 2009 Lecture 2. Building the NCBI C Toolkit and Applications on Unix. -C. Hogue (See Instructions page and attached below the linux-x86.ncbi.mk updated make file for Linux for the OpenGL libraries) Sat Nov 7 2009 Lecture 3. Platform Independent C Code. -C. Hogue (Attached below: 091107_Lecture3_Platform_Independent_Code.ppt and example code readseq.tar.gz ) Sat Nov 14 2009 Lecture 4. FASTA Sequence Format and the BLAST ReadSeq/FormatDB API. FETCHSEQS PRACTICAL: Processing Arguments: Strings, Memory, Variables, Pointers, Casting and Linked Lists. -C. Hogue Sat Nov 21 2009 Lecture 5. More C Toolkit and ASN.1: Web Server, Vibrant GUI Programs and FASTA to ASN.1 interconversion. -C. Hogue. (Attached below: 091121_Lecture5_More_C_Toolkit_and_ASN1.ppt and fasta to ASN.1 conversion example code fasta_asn1_converter.tar.gz) Sat Nov 28 2009 Postponed to Sun Nov 29 at 10am
Lecture 6. Asn.1 Continued, Concurrent Version System (CVS), and the Gnu Debugger -C. Hogue (see Biological Sequences in the original NCBI C toolkit manual) Sat Dec 5 2009 Lecture 7. Practical Exercise: Building the NCBI C Toolkit and Applications on Windows -C. Hogue Instructors:
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INTENSIVE COURSE - Advanced NCBI C Toolkit, MySQL, NCBI C++ toolkit and Java/J2EE Dec 7- 15, 2009 Venue S1A Computer Room, Level 4. Hours: 2 Daily 90 minute lectures start promptly at 9:00am and 1:00pm Practical work time from 11:00-12:00 and 3:00-6:00pm Prerequisite: NCBI C Toolkit Basics RESOURCES NCBI C Toolkit Book NCBI C++ Toolkit Cross Reference MySQL, MySQL C API, MySQL C Howto Connect in Linux Online Book Chapter on MySQL C API in MySQL (Fourth Edition) by Paul DuBois 2008 MySQL++ Manual WxWidgets, WxWidgets Documentation Worked Examples are now up.
Monday Dec 7 2009 Practical: Compiling NCBI Toolkit Applications on Windows Lecture 8. Biomolecular Structure - A Programmer's Perspective. -C. Hogue Attached below: 091208_Lecture8_Biomolecular_Structure.ppt Lecture 9. Molecular Modeling Database - MMDB-API - C Toolkit. -C. Hogue
Attached below: 091207_Lecture9_MMDB_API.ppt
Practical: Download 1OMD in binary ASN.1 and convert into PDB file with valtopdb.c. Attached below mmdb_test.tar.gz Tues Dec 8 2009 Lecture 10. Introduction to MySQL. -A. Ticoll Attached below: 091208_Lecture10_IntroMySQL.ppt Practical: MySQL Database Attached below 091208_Practical_IntroMySQL.ppt, data_set_ALL_AML_train.txt, table_ALL_AML_samples.txt Installation Instructions More MySQL info Lecture 11. NCBI C++ Toolkit Overview -A. Ticoll Attached below: 091208_Lecture11_NCBI_C++ToolkitOverview.ppt Practical Hints Wed Dec 9 2009 Lecture 12. NCBI C++ Toolkit - XML Schema from ASN.1. -A. Ticoll Attached below: 091209_Lecture12_C++Toolkit_ASN1_XML.ppt Practical: Object Manager Browsing C++ Toolkit Source: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/
Lecture 13. Accessing Databases with the NCBI C++ Toolkit and the C++ MySQL interface. -A. Ticoll Attached below: 091209_Lecture13_MySQL++.ppt MySQL++ Install Practical - Integrated C++ Toolkit Thurs Dec 10 2009 Lecture 14. NCBI C++ Toolkit - Web and Network Connection Code. -A. Ticoll Attached below: 091210_Lecture14_C++Toolkit_Connection.ppt Live Demo - Creating a Simple Java Application
Attached below: 091210_Lecture15_Intro_to_Java_and_Design_Patterns.ppt
091210_HelloWorldJavaEclipseCommand_Demo.ppt
Fri Dec 11 2009 Lecture 16. Introduction to JEE and Web Application Development. -J. Salama Live Demo: Creating A Simple Spring MVC Application
Live Demo: Creating A Simple Dynamic Web Application
Attached below: 091211_Lecture16_Intro_to_JEE_and_Web_App_Development.ppt
091211_HelloWorldSpringMVC_Demo.ppt
091211_HelloWorldDynamicWeb_Demo.ppt
Lecture 17. Introduction to XML and XSLT. -J. Salama Live Demo: Working with ASN.1 in Eclipse
Live Demo: XML, XSD, XSLT & XPath
Attached below: 091211_Lecture17_ Intro_to_XML_and_XSLT.ppt
091211_Working_with_ASN1_in_Eclipse.ppt
091211_XML_XSD_XSLT_XPath_Demo.ppt
Sat Dec 12 2009 Lecture 18. Using XML in Java -J. Salama
Live Demo: XML Binding in Java
Attached below:
091212_Lecture18_Using_XML_in_Java.ppt
091212_XMLBinding_in_Java_Demo
Lecture 19. Introduction to Lucene Text Indexing. -J. Salama
Live Demo:
Attached below: 091212_Lecture19_Intro_To_Lucene_Text_Indexing.ppt 091212_LuceneCommand_Demo.ppt
091212_XMLProcessing_in_Java_Demo.ppt
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RCE in Mechanobiology Advanced Bioinformatics Software Development Workshop
Subpages (15):
Build Instructions
Building the NCBI C Toolkit and Applications on Windows
CVS and GDB for the NCBI Toolkit
FetchSeqs Practical
GUI Example - Vibrant
Lecture 10 Installation Instructions
Lecture 11 Practical Hints
MySQL notes
MySQL++ Install
NCBI C++ toolkit build with Cn3D and wxWindows
Practical 12 Object Manager
Practical 13
Practical 14
SETUP JAVA ECLIPSE ENVIRONMENT
Web Server Example
Attachments (31) |