I am always fascinated by the insert kingdoms... not that I will keep them as pets, in fact, I am scared of most of them =P. However I always find them rather intelligent.
Recently I came across this article from National Geographic and I couldn't help wondering what else have we not discovered from this tiny sized kingdom to make our world more efficient.
Quoted:
"Ants aren't smart, ant colonies are." A colony can solve problems unthinkable for individual ants, such as finding the shortest path to the best food source, allocating workers to different tasks, or defending a territory from neighbors. A individual, ants might be tiny dummies, but as colonies they respond quickly and effectively to their environment. They do it with something called swarm intelligence.
Hmmm... sounded very similar to social computing and all the Web 2.0 'technologies' (well, not exactly the same but hey, that's how del.icio.us works!). Just a note, ants have been doing so for 140 million years.
Another interesting one... from Science - a theoretical biologist, Halloy, has successfully created robot cockroaches to mingle with the real 'peers' and even persuaded many of their insect 'peers' to hide in an unconventional place. With this, scientists speculate that this can be developed into a 'powerful' pest control. Well, as I have said from the beginning, the insert kingdoms are intelligent so we will see if it became reality. Whichever the case, it is interesting to know how inserts think...
Friday, November 16, 2007
Institute for System Biology
Overview of Institute for System Biology(ISB)
System Biology is the study of the interactions between genes, proteins and biochemical reactions which give rise to life. System Biologist focuses more on all the components and the interactions among them instead of analyzing individual components. These interactions are the main reasons for the form and function in an organism.
System Biology came from the result of the genetics “catalog” provided by the Human Genome project. Another reason is the increasing knowledge of how genes and their resulting proteins give rise to biological form and function. The internet aided the study of System Biology with ease as it allows researchers to store and distribute massive amounts of information.
Overview of HUMAN PROTEOME FOLDING PROJECT
The Human Proteome Folding Project, which use the power of computer to predict the shaping of Human proteins for which are still new to researcher. The researchers hope to learn something from this shape as the shape of the proteins show how they function inside our body.
The project starts with human proteins from the human genome. We will fold the proteins that have no known structure. By using the Rosetta structure prediction, we can predict the structures (fold) of these unknown proteins. Rosetta uses a scoring method to search through huge numbers of possible structures and choose the best among all. Then we will cross-match the predicted structures with existing protein structures using the X-ray crystallography and NMR-spectroscopy to see if the prediction has been seen before. If a match is found, the researcher will use various methods to get the function of these unknown proteins.
My Conclusion
Systems biology is advancing in a fast pace; we are currently at the turning point in further understanding of what the future holds for biology and human medicine. The ISB is the pioneer of this new opportunity.
Source:
http://www.systemsbiology.org/
http://www.systemsbiology.org/Technology/Data_Visualization_and_Analysis/Human_Proteome_Folding_Project
System Biology is the study of the interactions between genes, proteins and biochemical reactions which give rise to life. System Biologist focuses more on all the components and the interactions among them instead of analyzing individual components. These interactions are the main reasons for the form and function in an organism.
System Biology came from the result of the genetics “catalog” provided by the Human Genome project. Another reason is the increasing knowledge of how genes and their resulting proteins give rise to biological form and function. The internet aided the study of System Biology with ease as it allows researchers to store and distribute massive amounts of information.
Overview of HUMAN PROTEOME FOLDING PROJECT
The Human Proteome Folding Project, which use the power of computer to predict the shaping of Human proteins for which are still new to researcher. The researchers hope to learn something from this shape as the shape of the proteins show how they function inside our body.
The project starts with human proteins from the human genome. We will fold the proteins that have no known structure. By using the Rosetta structure prediction, we can predict the structures (fold) of these unknown proteins. Rosetta uses a scoring method to search through huge numbers of possible structures and choose the best among all. Then we will cross-match the predicted structures with existing protein structures using the X-ray crystallography and NMR-spectroscopy to see if the prediction has been seen before. If a match is found, the researcher will use various methods to get the function of these unknown proteins.
My Conclusion
Systems biology is advancing in a fast pace; we are currently at the turning point in further understanding of what the future holds for biology and human medicine. The ISB is the pioneer of this new opportunity.
Source:
http://www.systemsbiology.org/
http://www.systemsbiology.org/Technology/Data_Visualization_and_Analysis/Human_Proteome_Folding_Project
Mascot
Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases.
While a number of similar programs available, Mascot is unique in that it integrates all of the proven methods of searching.
These different search methods can be categorised as follows:
- Peptide Mass Fingerprint in which the only experimental data are peptide mass values
- Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query
- MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides
Project which uses mascot - HUPO Brain Proteome Project Pilot Studies
Purpose of this project:
Proteomics studies driven by large consortia often led to heterogeneous data due to different strategies, techniques and equipment. Nevertheless, results have to be implemented into one database to assure a common, standardized interpretation. This is why this pilot study is initiated as high degree of standardization are extremely important in order to obtain reliable results.
Objective of this project:
To come out a solution to data standardization by analyzing data by four different search engine (Mascot,Sequest,PFF-Solver and Phenyx).
For more information, visit
http://www.medizinisches-proteom-center.de/lehre/poster/HUPO/Christian_Stephan_HUPO_2005.pdf
For information on mass spectrometry, visit
http://bioisit.blogspot.com/2007/11/mass-spectrometry.html
References:
http://www.matrixscience.com/
http://www.hbpp.org/
Thursday, November 15, 2007
Gel Electrophoresis
What is Gel Electrophoresis?Learn about me here in a FUN way!
Gel Electrophoresis is a method to seperate DNAs or proteins by an electrical charge through a gel, thus the name.
DNA is a negatively charged molecule, thus it is moved by electric current from the negative end to the positive end. DNA moves in agarose that works like a sieve. The DNA is then seperated according to their size, the smaller or shorter fragments will move faster towards the postive charged end.
A video on how agarose gel electrophoresis is performed:
Proteins are commonly seperated by using polyacrylamide gel electrophoresis (PAGE) to characterize individual proteins in a complex sample or to examine multiple proteins within a single sample.
For more info on Polyacrylamide Gel Electrophoresis
The electrophoresis procedure can be a starting point for future additional identification and isolation of DNA fragments.
An example of 1D gel electrophoresis:
PS: Click the image if it's not moving.
An example of 2D gel electrophoresis:
Current projects:
From the University of Bristol, Proteomics Facility.
One example is Protein Expression Analysis.
Objective: To be able to elucidate proteins which may be downstream of galanin and therefore play important trophic roles following nerve injury.
More!
2D Gel Matching
Department of Computer Science, Free University of Berlin
Basically, this project is to identify protein information on a gel image and compare it with another gel image which already has the information on the identity of the proteins is performed.
Visit here for more information.
Gel Electrophoresis is a method to seperate DNAs or proteins by an electrical charge through a gel, thus the name.
DNA is a negatively charged molecule, thus it is moved by electric current from the negative end to the positive end. DNA moves in agarose that works like a sieve. The DNA is then seperated according to their size, the smaller or shorter fragments will move faster towards the postive charged end.
A video on how agarose gel electrophoresis is performed:
Proteins are commonly seperated by using polyacrylamide gel electrophoresis (PAGE) to characterize individual proteins in a complex sample or to examine multiple proteins within a single sample.
For more info on Polyacrylamide Gel Electrophoresis
The electrophoresis procedure can be a starting point for future additional identification and isolation of DNA fragments.
An example of 1D gel electrophoresis:
PS: Click the image if it's not moving.
An example of 2D gel electrophoresis:
Current projects:
From the University of Bristol, Proteomics Facility.
One example is Protein Expression Analysis.
Objective: To be able to elucidate proteins which may be downstream of galanin and therefore play important trophic roles following nerve injury.
More!
2D Gel Matching
Department of Computer Science, Free University of Berlin
Basically, this project is to identify protein information on a gel image and compare it with another gel image which already has the information on the identity of the proteins is performed.
Visit here for more information.
Mass Spectrometry
Brief Description:
The general meaning for Mass Spectrometry is an analytical tool used for measuring the molecular mass of a sample. In Bioinformatics, Mass spectrometry plays an important role in Proteomics and will still be a key technology in a foreseen future. "Structural information can be generated using certain types of mass spectrometers, usually those with multiple analysers which are known as tandem mass spectrometers. This is achieved by fragmenting the sample inside the instrument and analysing the products generated." quoted from Introduction to MS link source below. Mass Spectrometry data are used in Mascot.
Ongoing Project:
Molecular Characterization of the Lipidome by Mass Spectrometry.
Aim: Designed for high-throughput oriented lipid analysis by integrating robotic sampling, lipid species-specific mass analysis and software-assisted deconvolution of spectral data.
Improvements in mass spectrometric technology have proved highly efficient for the characterization and quantification of molecular lipid species in total lipid extracts. This methodology is less timeconsuming compared to that of conventional methods(e.g highperformance liquid chromatography, thin-layer chromatography (TLC), and gas chromatography) and requires less sample amount because of its higher sensitivity and specificity.
Uses 2 type of mass spectrometry
- electrospray ionization mass spectrometry
- hybrid quadrupole time-of-flight (QqTOF) mass spectrometer
The whole of Ongoing project is quoted from the Project Information link source below.
My Thoughts:
With these new researches for Mass Spectrometry, the future generation will have easier time to analyze proteomics and other small molecules not only in Bioinformatics, but also other related fields. There is even a blog for Mass Spectrometry with related videos and a link which shows mass spectrometer protecting soldier in Iraq.Source:
Introduction to MS
MPI.CBG research
Project Information
Text Mining Technique
Text mining or text data mining is the process of extracting useful information from text.Through techniques of dividing patterns and trends high quality information can be obtained from input text.
Andrew Clegg of the Shepherd Group is developing methods of extracting bioinformatics data resources (E.g. molecular biology journal articles) using text mining technique. As there is some challenge in the area of recognition and identification of gene and protein names, a system called BioNERD is developed and integrated with the system.
Another problem he has is with natural language, there is many different ways of expressing one something.
His Solution is : "parsing the sentence with a phrase-structure parser, mapping the resulting syntax tree into a dependency graph where each node is a word and each arc a grammatical relation (see image), and identifying subgraphs covering two or more entities which are characteristic of genuine relationships." - quoted from his site.
In layman terms , using a technique to split the sentence into smaller bits and determining their relationship with each other and thus drawing out information.
Once completed BOOTStrep will be available for public use and will be available in a number of languages.Further more the system itself will be able to validate its data automatically for accuracy and originality.
With both of these technologies in place we will be able to extract valuable information from journals and other documents without actually reading them thus saving us precious time to do our coding and other research. With the ever growing database of biological information we really need these services to help us keep track of what biological knowledge we have accumulated over time, else much of these discovery could be over looked due to the lack of human effort of actively seeking the discoveries that others have newly found.
sources : Andrew B. Clegg projects . BOOTStrep project website
Friday, November 9, 2007
IT3121 2007S2 research and blog
Dear IT3121 2007S2 students,
I hope by now you all have started reading or researching on the term that is assigned to you (see the following table). The main purpose is to study the latest research or interesting projects (in the field of bioinformatics) and give your comments.
You can directly post an entry to this blog or link to your own website or blog. You can use animations, graphs, pictures or even quotes from famous researchers, just remember to include the citation and the necessary acknowledgement.
Looking forward to reading your blog and research =)
I hope by now you all have started reading or researching on the term that is assigned to you (see the following table). The main purpose is to study the latest research or interesting projects (in the field of bioinformatics) and give your comments.
You can directly post an entry to this blog or link to your own website or blog. You can use animations, graphs, pictures or even quotes from famous researchers, just remember to include the citation and the necessary acknowledgement.
Looking forward to reading your blog and research =)
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