Looking Forward

User-friendly

Fast

Usable by users of all academic levels

Reduces Time?

Reduces Cost $$$$

Development of bioinformatics tools

Margaret Dayhoff publishes the Atlas of Protein Sequence and Structure

Wilbur and Lipman develop sequence database searching algorithm

Protein Structure

3D Visualization

- PyMOL

Python

programming

language!

Molecular!

STRAP

What is it really?

Comprehensive software suite to view proteins

Contains a large set of tools and functionalities

Multipurpose

What can it do?

Supports many protein file formats

Is it REALLY that good?

CONCEPTS

Allosphere

Insanely expensive

art project

THANK YOU!

“If I have seen further than others, it is by standing upon the shoulders of giants.” – Sir Isaac Newton

1985

3 different contexts

Lipman and Pearson develop FASTP/FASTN – fast sequence similarity searching

1990

Protein evolution

Basic Local Alignment Search Tool (BLAST) is designed

Genetic Code

1983

1970,1980

Needle-Wunsch Algorithm published

Smith-Waterman Algorithm developed

1965

1950

1961

Frederick Sanger announces the sequence of insulin, the first complete protein to be sequenced

Why did we need them

in the first place?

Christian Anfinsen showed that ribonuclease spontaneously refolded to regain its original enzymatic activity

Imagine if we were to use the methods of the past to perform DNA sequencing, how would that impact us?

Examples of students using DNA sequencer

What defines a bioinformatics tool?

• Introduction – Keith
• Development – Yuhan
• Tools – PyMol – Junhong
• Tools – STRAP – Ernest
• Visualization – Tomithy
• Future - Yuanru

A development and implementation tool that provides a bridge to enable access, use and management of data

Why do we need them?

What is a bioinformatics tool?

What are the requirements for a good bioinformatics tool?

BIOINFORMATICS

Tools & Techniques

Virtual Reality Chamber

Brings Researchers

Face to Face with

Their Data

DATA

SOUND

SIGHT

360-Degree

ALLOBRAIN

Looking forward!

"It's a place where you can use all of your senses" to find new patterns in data

Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data

omnitheater

Designing a large-scale multimedia environment to deliver rich, coherent, interactive, high-resolution 3D video and audio streams from voluminous amounts of scientific data, all in real-time, was a non-trivial computational and systems engineering task that involved a significant number of faculty from diverse disciplines.

+

Killer new

research vehicle

• Molecular visualisation software
• Developed by Warren Lyford DeLano

Author: Christoph Gille

Structure-based

Sequences

Alignment

Program

What's Good?

• Supports many file formats (PDB, MOL etc.)
• Runs on many op. platforms
• Can create movies
• Simple, yet able to create great graphics
• Many in-built functions
• PyMOL Wiki!
• It's free! (for students and teachers..)

Interact

with datas

http://www.bioinformatics.org/strap/#START

What's Not-so-good

• Boring interface
• Need to have technical knowledge to do really fancy stuff
• Cannot predict interactions between molecules

Sneak Preview!

External GUI

PyMOL viewer

We are 14,000km away ):

Ability to analyse at the atomic level

Worth?

Nice graphics (:

Translation

Sequence alignments

eg. ClustalW

i.e nucleotide to amino acid sequences

Nucleic acids + proteins are no longer mere

letter permutations!

an incredible toy

Structure based alignment of proteins

Structural

Prediction

e.g TM-align

3D- visualization

• DSSP format

STRAP

• PDB format

e.g Pymol, Rasmol, Jmol

• FASTA format

Phylogenetic

trees

Killer research tool

VS

eg. Genebee

Use all senses to find new patterns in data

Collaborate

with planetariums

Researchers shrunk

to the size of their data

Domain-specific applications that can be used in other display and computing environments

Transfer

design knowledge

Create display and interaction environments that scale appropriately from the AlloSphere to display walls to desktop to mobile environments

Software

infrastructure

Basic bioinformatics tools

Unable to visualize processes

Limitations

Advantages

Not realtime

Professor JoAnn Kuchera-Morin

WHAT'S NEXT????

Unable to view interactions

Saves

time

Minimizes

data loss

Convenient

Biodata mining &

Visualization

Tools are an extension of the mind

Brilliant New Bioinformatics Tools!!!

Abstraction

Overlaying

information

Manipulation of

information

Manage complexity

Compelling

sensory apparatus

Spatial

relationship & geometry

Systems and relational