RCE in Mechanobiology Advanced Bioinformatics Software Development Workshop

OFFICIAL SCHEDULE (Revised 16 Dec 2009)
C toolkit Build Instructions Revised 29 Dec 2011

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-**.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 ServerVibrant 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:




 


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
Practical: Web-based CGI App

Lecture 15. Introduction to Java and Design Patterns. -J. Salama
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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Christopher Hogue,
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data_set_ALL_AML_train.txt
(1999k)
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Dec 7, 2009, 3:34 AM
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fasta_asn1_converter.tar.gz
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Christopher Hogue,
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linux-x86.ncbi.mk
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Christopher Hogue,
Nov 6, 2009, 12:34 AM
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mmdb_test.tar.gz
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Christopher Hogue,
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readseq.tar.gz
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table_ALL_AML_samples.txt
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