18th - 20th April, 2006

Hinxton Hall
Wellcome Trust Genome Campus
Hinxton, Cambridge
United Kingdom

Bioinformatics Software Development Course

Schedule


	Day 1	Day 2	Day 3
	Coffee available at 9.00	Coffee available at 9.00	Coffee available at 9.00
	The main objective is to get an overview of EMBOSS programming and become familiar with string-handling. Your main task is to implement a program to perform some simple string manipulation tasks.	The main objective is to deepen your knowledge of programming and software development under EMBOSS. Your main task is to adapt your program to incorporate the functions of several existing EMBOSS applications.	The main objective is to get a feel for some of the advanced programming features. This day is open-ended; you can pick tasks to learn about the advanced features, or consolidate what you did on the previous days.
9.15	"Introducing EMBOSS" + Practical 1 To begin, you'll learn how to install and compile EMBOSS	"The AJAX Library & The Software Cycle" + Practical 7 Here you'll get an overview of the AJAX low-level library functions. But there's much more to software than just coding; you'll plan your days work considering your design and the essential steps for efficient development.	"Data Input : Using Features" + Practical 8 Features are specific regions of interest in a biological sequence. You'll learn how EMBOSS supports a variety of common feature formats and modify your program to read in sequence features from file.








10.00	"Navigating EMBOSS" + Practical 2 EMBOSS is big. Learn how to efficiently navigate the package and its libraries to find stuff you need.	"ACD files : Intermediate Skills " + Practical 7 cont. It's easy to create a friendly and intuitive application interface using the ACD syntax. This practical shows you how.	"Data Output : Using Reports" + Practical 9 The standardisation of application input / output is essential for interoperability. You'll learn how EMBOSS achieves this by modifying your program to use one of the standard EMBOSS report formats.









	Coffee available at 10.30	Coffee available at 10.30	Coffee available at 10.30
11.00	"Your first EMBOSS Application" + Practical 3 Learn the basic steps needed to develop any EMBOSS application by implementing helloworld!* under EMBOSS.*	"Sequence Handling" + Practical 7 cont. ACD files support various biological data types and many file formats saving you huge effort. You'll deepen your knowledge of ACD by modifying your program to handle real biological sequences from any source.	"Objects, Pointers and Memory Management" + Practical 10 To support new biological datatypes you'll need a deeper knowledge of memory managment under EMBOSS. You'll learn how to program your own data structures and functions for their manipulation.









	Lunch from 12.00 till 13.00	Lunch from 12.00 till 13.00	Lunch from 12.00 till 13.00
13.00	"Introduction to Objects using Strings" + Practical 4 EMBOSS programming objects (C data structures and functions) form the core of the EMBOSS libraries. You'll get a gentle introduction to objects by adapting helloworld.c to do some simple string manipulations.	"ACD Files : Advanced Skills" + Practical 7cont. Defining an application interface may involve calculations, conditional statements and the use of variables and menus. You'll learn how EMBOSS supports these operations and lets you probe the attributes of input datatypes such as sequences.	"The NUCLEUS Library" + Practical 11 The NUCLEUS Library incorporates various algorithms for molecular biology. This practical will give you a taste of what's available.









14.00	"ACD Files : Basic Skills" + Practical 5 EMBOSS allows very flexible definition of application interfaces via the ACD language. You'll get a gentle introduction to ACD programming by adapting your application for user-defined input and output and file-handling.	Practical 7 cont. You will continue work on your program and add enhanced functionality to the ACD file.	"Free For All" Finish off your program or go back to a topic that interests you most.









	Coffee available at 15.00	Coffee available at 15.00	Coffee available at 15.00
15:00	"EMBOSS String Handling" + Practical 6 Efficient string handling is fundamental to molecular sequence analysis. You'll deepen your familiarity of the powerful AJAX string library by way of a worked example.	"Software Consolidation" + Practical 7 cont. Learn how to consolidate your work through coding standards, documentation and quality assurance tests. You'll apply these methods to uour application.	"Free For All" The EMBOSS Developers will be around to discuss your own projects and collaborations.









16.00	"Free For All" Finish stuff off or review material for the next day.	"Free For All" Finish stuff off or review material for the next day.	"Free For All" Finish stuff off. Talk to the EMBOSS team. Or go to the pub / home.









17:00	Day 1 Close	Day 2 Close	Course Close

Last modified in 2005 by Jon Ison.