Last week I finished my Chemistry homework. My topic was on the relationship of cloud computing and bioinformatics. Both of the subject are relatively new and interesting. I got a lot of information out there in the internet. So just to contribute back to the community, here is my paper.
Bioinformatics is basically the application of computer science and information technology in the field of Biology, Medical Science and disease research. Bioinformatics mainly deals in devising algorithms, computing models, storing and structuring research results, modeling and simulating different cellular models etc. Bioinformatics also relates to inventing new computing systems. Neural computing system is such theoretical computing model in which the circuits of the computer resemble the synaptic connections those are found in human brain. Hence, increasing the computing power of a machine exponentially.
Cloud computing is the use of parallel computing over the Internet. It is a system in which a task requiring huge processing power, is distribute evenly to a number of computers or server and processed simultaneously. This significantly reduces the time required for the processing.2
The difference between cloud computing and traditional grid computing is that, cloud computing is treated as a utility service. The concept of cloud computing is similar to that of buying electricity from the national grid instead of having to set up a small power station at home. Cloud computing offers same services and utility that a client could ask from his own data center. Only difference is, he does not need to setup a data center in order to use one. The 'service' can be accessed from anywhere, any time, from any device (computer, laptop, iPads or Mobile phones). 17
As mentioned before, bioinformatics is simply the application of information technology in the field of biology and medical science. Currently, “protein folding” is a common term. It mainly discusses the possible ways a protein may organise itself or in short the way it will ‘fold’.
Protein are known to be the ‘workhorse’ of biology. they are found in every cell of out body and they control all the functions in our body. Proteins are basically long chains of amino acid that can combine practically in infinite number of ways to form a protein. for each protein there is a definitive function and structure. structure of the protein means the particular way amino acids combine with each other. based on the combinations of amino acid the function of proteins are determined. now proteins perform various functions inside our body. some protein deliver energy to our muscles, other carry sensory signals to our brain etc. the folding of protein is a defined process (which we do not have a clear perception on!).
Now if for some reason, a protein folding goes wrong, we fall victim to various diseases. diseases such as Alzheimer, cancer, AIDS are because of misfolding of proteins. since we do not know exactly how these ‘misfolding’ happens, we are not yet able to find a cure to such diseases. if we could figure out the exact process, cancer would vanish from Earth.
Clearly, the computational speed of machines are much more than that of a human. so we have define an algorithm to do the work for us. this is where bioinformatics come in. bioinformatics studies the way we could use technology much more effectively to find solutions to our problem. bioinformatics deploy various techniques, algorithms and computational system to speed up the calculation process. this is why bioinformatics is so important.14
the permutation algorithms take a long time to produce outputs in an average computer. that is why such calculations are performed on powerful computers such as a medium size server.
Latest researches in the field of medicine, biology, chemistry has a huge demands for powerful computational system. Computer system are required to perform complex calculation and simulation in order to obtain result. Most of the universities facilitating such research have their own server system to perform complex calculations. These servers, despite of having very high number of core (processors), sometimes fall behind schedule while researchers anxiously awaits their turn to use the common parallel processing system of the university. Few of the cases, the processing power of these servers are insufficient. In such cases, the necessity of having additional computing power arises.
Not in all the cases, additional computing power can be managed for a project. It may because of limited space or fund. In such cases necessity of a third party vendor is felt. This third party offers their computing system in form of cloud computing.
Technology has helped us to progress in every field of our life. It has eased our banking system, workplace, education and every other field we can think of. In the complex field of biology, medicine and medical science, the application of computer technology becomes absolute necessity. Here are few reason why cloud computing can become the prime need for bioinformatics. some of the benefits are given below,
Large Database:
Cloud computing system could offer a smart system to store, review, share and revise existing data on various research. It can make the data accessible from any corner of the world. Thus enabling the researchers to know the necessary data for their research. It will also keep away researchers from doing a research which has already been done.
Collaboration:
Cloud computing offers an interesting platform for collaborated projects, enabling researchers overseas to contribute and indulge in discussions in real time.
Security:
Security and privacy for the data stored in cloud system has been hot topic since the appearance of cloud computing. thanks to various contributors, Data stored in cloud servers now have devised a system which makes the cloud highly secured place to store the data. 4
normally, to provide security to any data, the data itself is encrypted. only the with The encryption key the data can be decrypted and used at a later time. Without the encryption key, the data is out of any danger.5
However, when the data was stored in the cloud the key had to be saved some where. the concept of cloud computing tells that even the key has to stored in the cloud, not on client’s machine to ensure the portability that the cloud promises. But, storing the key on the cloud itself, side by side with the data remained a security threat.
Now the problem has been solved. the solution involves splitting up the key into two separate key. A system which is already in use in vaults, found in large banks to safe guard the money inside. One key resides in the cloud and the other with the client. when the data needs to be accessed, both of the keys are needed. However, the key residing in the server is itself encrypted, which can only be decrypted by the other key residing with the main client. as a result, the data stored in the cloud are now safest as they can be.
No initial funding and maintenance cost:
In order for an organisation to set up a data centre, enormous amount of fund is required to invest in the setup of the data centre. The step involves acquiring space, building the required infrastructure and last but not the least, setting up the equipments. then a team of technicians are required to have the data centre running. In total it requires enormous amount of funding to keep things get started and running.
Cloud computing services, such as Amazon EC2 offers various organisations, the same service for fixed fee. 18
So, in short run cloud computing can prove to be a lot cheaper and efficient.1
Efficiency:
Private data centers, such as the servers of a university, are accessible to only a fixed group of people. Those who are able and interested to use the existing infrastructure of parallel computing, have to apply and go through a system and wait for their turn. This period of latency may be from a few days to a month of two. To sum it up, number of people have to waste their valuable time.
The other way around is also true. There may be a period when no one needs the service of parallel computing. The computing system has to remain idle. but the cost of maintenance don’t go away, the cooling system and the technicians have to be on their toes.
So we see, private grid networks are not always efficient.
Public grid networks, Cloud Computing in this case, has few advantage. Since the service is offered to a large group of people, the machine itself doesn’t remain idle for long. Hence the maintenance cost is justified. Again, such system have advanced load management system, so that people waiting to have their data processed, do not have to wait for long. Overall, cloud computing offers maximum efficiency.
Elasticity:
On servers, there are some occasional spikes. For number of reason the number of user may increase without a warning. Cloud system has the best load management system. on demand it can reallocate more resources to the demanding task and still able to finish it in due time. That is to say, under stress, it behaves like an elastic and adapt to the situation.
Reliability:
Cloud system are the most effective and reliable system around. Clients are not responsible for the maintenance and upgrade of cloud system. the company offering the service manages all. Which also means, the user do not need to bother about going through the complex process of upgrading various background system.
Although application of cloud computing in the field of bioinformatics may seem a fantastic idea, the technology itself is in its infant state and has minor flaws. They are,
Internet dependency:
Cloud services are greatly dependant on Internet service. Literally, the service resides on the Internet. Any failure in Internet connection will result in failure of cloud service.
Short run Benefits:
Cloud computing is relatively a new topic in the computing world. It has been creating buzz since 2006. It is a system that promotes the concept, “software as a service”. However, all the economical statistics suggests that, cloud services are only beneficial and economic for a short period of time. It is not feasible for a short period of time.
security:
Security of cloud system has been a hot topic of debate for technology experts. They are not content with the internal architecture of the cloud system. Many research has been made and there have been some shocking revelation, how cloud systems can be cracked.
Fortunately, most of the cyber attacks were launched equally powerful grid system. In real world, it is not very likely to face such large scale attacks. Not to mentions, countless projects and researches are in motion to make the cloud system more reliable and safe.
Cloud computing hols a lot of promise in the domain of emerging computing technology. currently, only business organizations are using the benefits of the new system. bioinformatics is an important branch of science. we need this branch to evolve for our own benefit. since evolution of bioinformatics is directly dependant of computing power, it can certainly benefit of the cloud system. Although there are some minor concerns relating to the new technology, hopefully,such problems will be solved in the coming future. cloud computing has its own set of advantage and disadvantages. if we can figure out the optimum configuration for it, than the field of bioinformatics will be greatly benefited.
Possibilities of Cloud Computing in Bioinformatics
Bioinformatics:
Bioinformatics is basically the application of computer science and information technology in the field of Biology, Medical Science and disease research. Bioinformatics mainly deals in devising algorithms, computing models, storing and structuring research results, modeling and simulating different cellular models etc. Bioinformatics also relates to inventing new computing systems. Neural computing system is such theoretical computing model in which the circuits of the computer resemble the synaptic connections those are found in human brain. Hence, increasing the computing power of a machine exponentially.
Cloud Computing:
Cloud computing is the use of parallel computing over the Internet. It is a system in which a task requiring huge processing power, is distribute evenly to a number of computers or server and processed simultaneously. This significantly reduces the time required for the processing.2
The difference between cloud computing and traditional grid computing is that, cloud computing is treated as a utility service. The concept of cloud computing is similar to that of buying electricity from the national grid instead of having to set up a small power station at home. Cloud computing offers same services and utility that a client could ask from his own data center. Only difference is, he does not need to setup a data center in order to use one. The 'service' can be accessed from anywhere, any time, from any device (computer, laptop, iPads or Mobile phones). 17
Importance of bioinformatics:
As mentioned before, bioinformatics is simply the application of information technology in the field of biology and medical science. Currently, “protein folding” is a common term. It mainly discusses the possible ways a protein may organise itself or in short the way it will ‘fold’.
Protein are known to be the ‘workhorse’ of biology. they are found in every cell of out body and they control all the functions in our body. Proteins are basically long chains of amino acid that can combine practically in infinite number of ways to form a protein. for each protein there is a definitive function and structure. structure of the protein means the particular way amino acids combine with each other. based on the combinations of amino acid the function of proteins are determined. now proteins perform various functions inside our body. some protein deliver energy to our muscles, other carry sensory signals to our brain etc. the folding of protein is a defined process (which we do not have a clear perception on!).
Now if for some reason, a protein folding goes wrong, we fall victim to various diseases. diseases such as Alzheimer, cancer, AIDS are because of misfolding of proteins. since we do not know exactly how these ‘misfolding’ happens, we are not yet able to find a cure to such diseases. if we could figure out the exact process, cancer would vanish from Earth.
Clearly, the computational speed of machines are much more than that of a human. so we have define an algorithm to do the work for us. this is where bioinformatics come in. bioinformatics studies the way we could use technology much more effectively to find solutions to our problem. bioinformatics deploy various techniques, algorithms and computational system to speed up the calculation process. this is why bioinformatics is so important.14
The connection between bioinformatics and cloud computing:
the permutation algorithms take a long time to produce outputs in an average computer. that is why such calculations are performed on powerful computers such as a medium size server.
Latest researches in the field of medicine, biology, chemistry has a huge demands for powerful computational system. Computer system are required to perform complex calculation and simulation in order to obtain result. Most of the universities facilitating such research have their own server system to perform complex calculations. These servers, despite of having very high number of core (processors), sometimes fall behind schedule while researchers anxiously awaits their turn to use the common parallel processing system of the university. Few of the cases, the processing power of these servers are insufficient. In such cases, the necessity of having additional computing power arises.
Not in all the cases, additional computing power can be managed for a project. It may because of limited space or fund. In such cases necessity of a third party vendor is felt. This third party offers their computing system in form of cloud computing.
Necessity of Cloud Computing in Bioinformatics:
Technology has helped us to progress in every field of our life. It has eased our banking system, workplace, education and every other field we can think of. In the complex field of biology, medicine and medical science, the application of computer technology becomes absolute necessity. Here are few reason why cloud computing can become the prime need for bioinformatics. some of the benefits are given below,
Large Database:
Cloud computing system could offer a smart system to store, review, share and revise existing data on various research. It can make the data accessible from any corner of the world. Thus enabling the researchers to know the necessary data for their research. It will also keep away researchers from doing a research which has already been done.
Collaboration:
Cloud computing offers an interesting platform for collaborated projects, enabling researchers overseas to contribute and indulge in discussions in real time.
Security:
Security and privacy for the data stored in cloud system has been hot topic since the appearance of cloud computing. thanks to various contributors, Data stored in cloud servers now have devised a system which makes the cloud highly secured place to store the data. 4
normally, to provide security to any data, the data itself is encrypted. only the with The encryption key the data can be decrypted and used at a later time. Without the encryption key, the data is out of any danger.5
However, when the data was stored in the cloud the key had to be saved some where. the concept of cloud computing tells that even the key has to stored in the cloud, not on client’s machine to ensure the portability that the cloud promises. But, storing the key on the cloud itself, side by side with the data remained a security threat.
Now the problem has been solved. the solution involves splitting up the key into two separate key. A system which is already in use in vaults, found in large banks to safe guard the money inside. One key resides in the cloud and the other with the client. when the data needs to be accessed, both of the keys are needed. However, the key residing in the server is itself encrypted, which can only be decrypted by the other key residing with the main client. as a result, the data stored in the cloud are now safest as they can be.
No initial funding and maintenance cost:
In order for an organisation to set up a data centre, enormous amount of fund is required to invest in the setup of the data centre. The step involves acquiring space, building the required infrastructure and last but not the least, setting up the equipments. then a team of technicians are required to have the data centre running. In total it requires enormous amount of funding to keep things get started and running.
Cloud computing services, such as Amazon EC2 offers various organisations, the same service for fixed fee. 18
So, in short run cloud computing can prove to be a lot cheaper and efficient.1
Efficiency:
Private data centers, such as the servers of a university, are accessible to only a fixed group of people. Those who are able and interested to use the existing infrastructure of parallel computing, have to apply and go through a system and wait for their turn. This period of latency may be from a few days to a month of two. To sum it up, number of people have to waste their valuable time.
The other way around is also true. There may be a period when no one needs the service of parallel computing. The computing system has to remain idle. but the cost of maintenance don’t go away, the cooling system and the technicians have to be on their toes.
So we see, private grid networks are not always efficient.
Public grid networks, Cloud Computing in this case, has few advantage. Since the service is offered to a large group of people, the machine itself doesn’t remain idle for long. Hence the maintenance cost is justified. Again, such system have advanced load management system, so that people waiting to have their data processed, do not have to wait for long. Overall, cloud computing offers maximum efficiency.
Elasticity:
On servers, there are some occasional spikes. For number of reason the number of user may increase without a warning. Cloud system has the best load management system. on demand it can reallocate more resources to the demanding task and still able to finish it in due time. That is to say, under stress, it behaves like an elastic and adapt to the situation.
Reliability:
Cloud system are the most effective and reliable system around. Clients are not responsible for the maintenance and upgrade of cloud system. the company offering the service manages all. Which also means, the user do not need to bother about going through the complex process of upgrading various background system.
Drawback:
Although application of cloud computing in the field of bioinformatics may seem a fantastic idea, the technology itself is in its infant state and has minor flaws. They are,
Internet dependency:
Cloud services are greatly dependant on Internet service. Literally, the service resides on the Internet. Any failure in Internet connection will result in failure of cloud service.
Short run Benefits:
Cloud computing is relatively a new topic in the computing world. It has been creating buzz since 2006. It is a system that promotes the concept, “software as a service”. However, all the economical statistics suggests that, cloud services are only beneficial and economic for a short period of time. It is not feasible for a short period of time.
security:
Security of cloud system has been a hot topic of debate for technology experts. They are not content with the internal architecture of the cloud system. Many research has been made and there have been some shocking revelation, how cloud systems can be cracked.
Fortunately, most of the cyber attacks were launched equally powerful grid system. In real world, it is not very likely to face such large scale attacks. Not to mentions, countless projects and researches are in motion to make the cloud system more reliable and safe.
Conclusion:
Cloud computing hols a lot of promise in the domain of emerging computing technology. currently, only business organizations are using the benefits of the new system. bioinformatics is an important branch of science. we need this branch to evolve for our own benefit. since evolution of bioinformatics is directly dependant of computing power, it can certainly benefit of the cloud system. Although there are some minor concerns relating to the new technology, hopefully,such problems will be solved in the coming future. cloud computing has its own set of advantage and disadvantages. if we can figure out the optimum configuration for it, than the field of bioinformatics will be greatly benefited.
References:
- http://www.biomedcentral.com/1471-2105/11/259
- http://www.youtube.com/watch?v=ae_DKNwK_ms
- http://cloudcomplete.blogspot.com/2012/01/day-12-pain-points-of-cloud-computing.html
- http://www.utdallas.edu/~mxk055100/courses/cloud11f_files/what-is-new-in-cloud-security.pdf
- http://www.pcworld.com/article/238503/is_cloudbased_backup_safe.html
- http://www.networkworld.com/news/2011/102611-security-cloud-252406.html
- http://www.youtube.com/watch?v=sE_OfVUUlaU
- http://www.informationweek.com/news/cloud-computing/229202319
- http://biostar.stackexchange.com/questions/132/experiences-with-cloud-computing-in-bioinformatics
- http://folding.typepad.com/news/2012/03/fah-simulations-lead-to-a-new-therapeutic-candidate-for-alzheimers-disease.html
- http://www.physorg.com/news168791338.html
- http://www.compukiss.com/articles/gamers-can-now-help-fight-disease-2.html
- http://www.slideshare.net/maikelm/disadvantages-of-cloud-computing
- http://folding.stanford.edu/#
- http://videos.howstuffworks.com/science-channel/28661-exploring-time-protein-folding-video.htm
- http://fold.it/portal/info/science
- http://www.wikipedia.org/wiki/cloud_computing
- http://aws.amazon.com/ec2/
