Bioinformatic Scientific Computing

Scientific Computing: Bioinformatics

Computer Science is a vague and endless space of ideas and functions. People unfamiliar with this term and industry are often confused on what a Computer Scientist refers too. A good example and practical use of the knowledge we have become accessible to is Bioinformatics.

For the standard scientist that we have all known commonly as docters, surgeons, pediatricians, chemist and biologist. They all deal with micro cellular levels of information. With modern technology we are now able to identify chromes of DNA and other cellular data. With technology advancing it has come to a point where there is too much of a workload that surpasses our capabilities. Bioinformatics is the study of those things listed. 

One of the key challenges biologists face today is the growth of information, which expands too fast for scientists to analyze it. It is difficult to find a way to organize, study, and draw conclusions from all this information. 

Genetic sequences that are commonly looked at are HIV, parkinsons and more. Using complex algorithms scientist are able to look at the differences between the nucleotide roots of the sequences. With all of these diseases and specimen presented to us there is an endless amount of research and cures that need to be made. 

This field is bound to grow and will end up curing cancer. A good example of results are the Human Genome Project which showed the world the potential in investing into biological research.

Sources: http://www.bioplanet.com/what-is-bioinformatics/

Computer Graphics

Graphics have come along way to the simple GUI bash shell that very few average joe's know of. Back in the day it was the only way to navigate through the system we know call the computer. Now people expect their computers to come with a "retina" display to see the clearest images that are now presentable. With a top tier computer and monitor people can see life like images before them. I remember sitting at my cousin's house playing a football game and my uncle though it was a real game being broadcasted live. With modern technology artists are using computers to draw and simulate movements to their characters.

From Pixars to Disney, there have been multiple innovations to the animated world. The technology that these people use are now presented to the common consumers through pretty devices such as Ipads and I touches where people can draw with a touch of their fingers.

The most adaptive concept that has been taken in as an essential to society is Image editing. This encompasses the processes of altering images. The original editing is done by, using tools such as an airbrush to modify photographs, or editing illustrations with any traditional art medium. It is traditionally known a photo retouching. Graphic software programs, which can be broadly grouped into vector graphics editors, raster graphics editors, and 3D modelers, are the primary tools with which a user may manipulate, enhance, and transform images. Many image editing programs are also used to render or create computer art from scratch.

For example: Guess which one is the original.

WIth all of these tools provided for free through the right services, the possibilities are endless. But at the same time it is not very easy to understand and use. That is why functions such as Photo effects are created which are preset conditions and arguments people use to upload their Instagram and Facebook pictures.

My Identity

With the rise of the data age, modern technology has become a prevalent tool in everyday life throughout the world. Pretty soon money will be tendered paperless and driving will become an automated function. With this in mind peoples personal identity are not safe from anyone. Not only that anybody can take over your identity easily which means our lives will not become original to ourselves. That is why Computer security has been the forefront of many people's concerns. Computer security is such a broad topic to talk about because it could fall into many fields such as cloud, network, or even cyber security. Instead I am going to cover the topic of attack bots.

With growing networks and competitors, there are many malicious software that are out there to attack your network. To prevent these measures of malicious attacks or people who have intentions of just abusing the system by up voting their own program or video by using automated tasks Captchas were invted.

The picture above shows a security measure that people use to make sure that the user logged in is not an automated bot. While this may sound harmful abusing the system is the same as if I would punch in at work. Leave for my whole shift and just come back to punch back out. With that in mind you can see how automated tasks and software can be bad. 

A brief history of CAPTCHA includes Turing Test. Alan Turing, sometimes called the father of modern computing, proposed the test as a way to examine whether or not machines can think -- or appear to think -- like humans. The classic test is a game of imitation. In this game, an interrogator asks two participants a series of questions. And sees the difference between machine and man.

Of course, with a CAPTCHA, the goal is to create a test that humans can pass easily but machines can't. It's also important that the CAPTCHA application. BUT one must keep in mind that software is built to combat these measures so different CAPTCHAs to different users. If a visual CAPTCHA presented a static image that was the same for every user, it wouldn't take long before someone could decipher the letters by spamming all the results and re use the same answer for all Capchay.

Source:CAPTCHA

ARTIFICIAL INTELLIGENCE

History of Computer Science

"History consists of past present and most importantly forgotten, the future"

Futures studies (also called futurology and futurism) is the study of postulating possible, probable, and preferable futures and the worldviews and myths that underlie them. The future is told every day, what people don't understand that time is just a measurement that humans use. It is a tangible number and can be equated as simple 1+1. A year simply represents the length of time it takes the Earth to rotate around the sun. Does anything happen to us within that year, that is any different than any year? No. Except for a few minor occurrences such as natural disasters and etc.

So here is a little trick for you skeptical folks. I am not predicting, but instead I know the future of this blog entry. You will skim through this with a puzzled face and proceed to write a pleasant comment about how you enjoyed my entry because no one seems to have a soul. 

To get back on track, there is no history without a future. Yes we all know the "history" of computers, and the only relevant one is when Apple released the Macintosh in 1984. For those who are intrigued by this Timeline. Refer to the purple underlined hyperlink. For those who are intrigued by relevant matters refer to the pictures surrounding us. Flying cars, personal robots, watches that act as cellphones, and most importantly google glasses. The future is here, it is funny because the mainstream of society back in the day believed we would have invented flying cars by now. Also what happened to my robotic soldiers or maids  All I see now are hybrid prius and a frisbee like object that cleans the floor.

So what does history have in mind for us scientist. Small scale maybe we are thinking a strapped in tablets that are powered by our blood. Or implanted chips in all of us so big brother can track our location and thoughts at anytime. All software and doc types become compatible with each other. Yes some of these things sound fun, but the biggest thing on everyone's mind is Artificial Intelligence. Yes we all know what that is, lets skip the cheesy dictionary definition. Some examples people can argue video game cpus, Siris and maybe even google search bar. These come close,, but aren't actually true AI, something like that could only come straight from a Sci Fi movie. True AI requires a computer to think for itself. So far, all computers simply derive results based on calculated values they are programmed to know. Machines are uncapable to learn beyond their programming or act in any way their weren't designed to do. Something real close though is Deep Blue which is a chess playing computer. I am definitely excited to see what the world has in mind for this though.

File Sharing

Sending large amount of files back and forth to one another happens everyday. Data is to another machine constantly, therefore file sharing applications such as email, and clouds are every day use. In fact I usually use email to send myself information between my laptop, phone or desktop more than emailing other people.
With the constant need to send files between machines if only their was a way to integrate all of these applications. At the moment I use two emails, one for social and one for business. An evernote for personal journal, a drop box for class and multiple google drive folders for classes and individual projects. With all of this data jumbling back in forth between my three devices it is hard to find anything at all. Most of the time it is just more convenient to just re download files. 

Luckily the development of a integrated cloud is on its way. While there are many options such as Cloud Magic it doesn't go further than email. Others can also say a drop box allows for a folder to be integrated into a computers library. But with 2Gb of free space and no real time update. Imagine any updates to be seen automatically without save such as google docs. A real time environment which makes you forget that your on another computer. The explanation doesn't justify the beauty of it. This is the future. Multiple devices, one account. One Desktop shared between home phone, tablet, tv, and computer.
Source: John DopeDo

A B C D XX Y Z

Information Presented

Data

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MLA APA
data structure.

              Information is presented in various ways. This essay itself is written in a certain format. In school teachers recommend either APA OR MLA format for research papers. The term Data structure refers to how one organizes their information. When people look at rate of changes the information is presented in a graph. Different learners have different preferences, but it is always necessary to keep items organized and readily available for access or change.

            In the technological industry Data Structures refer to a more specific definition. A Data structure refers to a object that store multiple elements of data. For example variables, collections, lists and array all store important elements that a user might process. It is important too understand that while one box may be just enough to hold everything, sometimes it is better to use multiple boxes to organize the objects better. At the same time for simple jobs maybe one box is enough.

       With this situation in mind studying data structures is not about completing a task instead it is about using the right tool for the job. Many considerations are made when creating one or picking an implemented one. Such as the size available, how many elements there are, how fast does it need to be to access, remove or find. All of these questions are important when encountering a problem. The algorithms are endless for this problem that is why it is important to understand the main concept of each data structure so tracing through each step in algorithm is not necessary. 
       
       It is imperative to review data structures when going to an interview now. In a Stack Overflow thread many experienced individuals why data structures are so important that interviewers demand an extensive knowledge in them before they can even begin to judge your qualifications. Understanding this concept means that one understands that there is no right answer. The topic of data structures is a great topic that explains in computer science there is NO right answer. Which is why many people are unable to enter this field.

Neo Hacking

Digital warriors

          Breaking the law for one's benefit has always been a interesting concept. But in today's physical actions such as robbing a bank or taking money from a cash register isn't necessary. The big money comes from white collar crimes, such as business scams and investment money embezzlement. Another form comes from just sitting at home and hacking networks to find any vulnerabilities. These hacker attacks are not a single person's action but have evolved to a group efforts. In article by Huffington Post it is explained how thousands of playstation network accounts were compromised by a large group of people.
           The concept of hackers and hacking has been around for much of the time the Internet has, and much like the Internet itself these terms have evolved over time. Originally hacking referred to attacks into private networks to access confidential information. But now the hacking that I and other future minded people refer to is completely different. Hacking use to be about stealing and destroying other people's work by creating virus and worm holes, but now it means creating a new entity from the materials provided.
         This is the way Hacking was meant to be, because like scientist, hackers in the early days were just motivated by curiosity. Hacking was a tool to learn what was inside a computer, how it ran and what made the network tick. From looking at the current windows machine Steve jobs was able to create his own. Like many children left alone to their own devices, I remember at young age breaking apart my clock and other small devices around the house hold and trying to putting them together. Hacking is no different, it allows a user to understand the structure of the subject they are looking at and with this knowledge are able to improve it or create a new prototype. 
      Generally the public may look at the word hacking in a negative connotation, but like anything in this world a tool can only be harmful in the wrong hands. A gun does not murder people, but instead a human does. In most cases, public defenders have guns to shoot another human, but only to protect themselves or the innocent citizens around them. A mischievous person however may use that gun to enact harm to themselves or to others. In the end hacking in its rawness quenches my thirst of knowledge. 

Open Source: Is it always free.The common terminology of open source refers to software that is offered for free for public personal or business use.Who contributes The creation of these products are usually a wide collaboration of people that work together in their personal time. Large projects may require the work of hundreds of people and they may receive small donations of users of the product. The open source projects can be found online and are always in need of help Products offered and why Pay? The most common software that is available are Unix and Linux distributions. According to market research it has a little bit under a 5% market share. With its competitors as the giant Microsoft and the fancy Apple. They also provide server distribution and they recieve a lot more attention than personal OS. With Linux distributions such as Red Hat theres is a long list of software for them. Such as Gimp which is a photoshop and Open Office for normal writing uses. The list is endlessSource: MarketResearch Source: MarketResearch So with all of these options what keeps up from using the alternatives. Almost everything now a day can be found for free either online or from an extra cd that your neighbor has bought. Yes there are various copyright laws and many infringements, but I do not know one person who does not download music. So the question is how far are you willing to take it. There are endless torrent websites that contain Adobe Master Suite to movies in theaters and etc. If you want something you will be able to find for free. While it is true that paying for a product allows you to redeem services, technical help and warranty which is necessary for companies. For personal use I pay for a very minimum of the software I use whether it is under a free trial license or just open source software such as notepad++.

Open Source: 
Is it always free.The common terminology of open source refers to software that is offered for free for public personal or business use.

Who contributes
The creation of these products are usually a wide collaboration of people that work together in their personal time. Large projects may require the work of hundreds of people and they may receive small donations of users of the product. The open source projects can be found online and are always in need of help

Products offered and why Pay?
The most common software that is available are Unix and Linux distributions. According to market research it has a little bit under a 5% market share. With its competitors as the giant Microsoft and the fancy Apple. They also provide server distribution and they recieve a lot more attention than personal OS. With Linux distributions such as Red Hat theres is a long list of software for them. Such as Gimp which is a photoshop and Open Office for normal writing uses. The list is endless
Source: MarketResearch

Source: MarketResearch

So with all of these options what keeps up from using the alternatives.

Almost everything now a day can be found for free either online or from an extra cd that your neighbor has bought. Yes there are various copyright laws and many infringements, but I do not know one person who does not download music. So the question is how far are you willing to take it. There are endless torrent websites that contain Adobe Master Suite to movies in theaters and etc. If you want something you will be able to find for free. While it is true that paying for a product allows you to redeem services, technical help and warranty which is necessary for companies. For personal use I pay for a very minimum of the software I use whether it is under a free trial license or just open source software such as notepad++. 

Agile: Moving forward

AGILE:

     What is Agile Development and what can it do for your team? 

   
In the past companies have conducted projects by using a Waterfall approach which would be considered starting from the beginning and moving step by step and advancing further. The problem with this though is that it does not allow as much room for change. Changing a phase one would mean redoing every other step after it that relies on the foundation. Apprehensively it is a very linear approach.

Look below and lets say a group approaches the same project with the same ideas and requirements in mind. But in order to achieve the final result they can take a different route. On the right side it shows the Agile chart, you can see how things are done almost at the same time and are iteratively processed. In the 2nd step the Initiation and Analysis are done at the same time and can be redone and change without delaying the timing of the project. 

The team that endorses and are the main founders of the Agile method has a Manifesto for Agile Software Development on their webpage. In it they describe in a short simple paragraph the idea and use of their method.

In the Work Place

Microsoft endorses the use of Agile for software development as stated in their Research Page. They prefer the variant that uses Scrum. They like the implementations on small scale projects but have doubts and concern on large projects with 20 members or more because the design is not as sustainable with such a large amount of people.

Overall when deciding which method to use whether Waterfall or Agile or any other development Model. Timelines, experience, resources, and requirements should be the factors in deciding your plan of action. With a Waterfall method, things can be executed faster and quicker so simple and small projects with definite requirements can be completed. With more freedom on a project I would prefer the Agile method because there would be more room for improvements or mistakes

1000+ Friends. Are they real?

In todays age there are social media websites such asLinked In, Twitter, Facebook, Google+ and this includes personal webblogs such as blogger, Xanga and Myspace. Now that we have the media websites covered you can't forget Instagram and Vine. With all of these options out there it is possible ot reach millions of people daily and if your content is interesting enough it can be sent viral and be surfaced on all of the interfaces listed above.

With all of these options available any entity or person must find it imperative to utilize these tools. But with over 1000 friends or followers on anyone of these websites are they really real or do they care about you? The answer is yes, although these aren't your closest friends or family member they are people who you have chosen to interact with and share your opinions with. Although most of them won't agree with you if %10 of them do then that means you have 100 supporters. To be able to reach certain destinations you will need the guidance or the help of certain individuals. Whether they chose to or not depends on their impression of me, but if they don't even remember me or have no way to contact me the opportunity will never cross.

Now that the use of social media has been necessary. With all the options out there why can't there be a single cloud interface that posts to everything. With Facebook there is now an option to link Instagram, Twitter, and other feeds so that people can see what your doing on each website. I preferably use Facebook and Instagram and Youtube separately. I find it weird when people get too personal on certain news feed. Which arises a huge topic of privacy which we'll talk about later. People think LinkedIn is more professional, but it really comes down too the audience you are targeting and what you post. Each website can be used for personal reasons or professional reasons. How I portray myself and the text, video and audio that I allow on my newsfeed.

But it is true that LinkedIn provides a direct access to job openings and companies.

Turning Binary into Art

QR codes: What.

Ever since the Android came out a new idea of thinking has been formed. To set them apart from a normal smart phone and they have created their own logo and brand. Most people now a days recognize the awkward green android robot. What he also came with is a Qr code which is the black hazy thing on the side. It pretty much resembles a bar code in a rectangular shape.

Qr codes is a not a new concept or design at all but this is the first time it is used for the general public. It is a step forward to automation. It is commonly seen on mail invoice and other logistic products. What it does, is provide the user an option to scan the picture using the devices camera and decode the Qr. It ultimately directs the user to a certain website or link and now has a coupon function. With tinkering on certain devices it now can do extra options to some devices. 

Media
I find it very interesting to display a blank document with a single Qr code and see who scans it. People are born curious and most of the time they will walk by and ignore it, but for the ones who do open it want to see something that interests them. According to a marketing news website over %50 of Americans own a smart phone now. They have become very affordable to the point where companies are offering them for free when signing up for a contract. With that in mind many companies have incorporated the Qr code into their advertising campaign. Some just need to realize that they need to display the code in visible areas, areas of service and display good content. It is the worst feeling when you get deceived into going to a website. If companies use good methods of use the Qr code will maintain its popularity otherwise like me, everyone else will just use the NFC "bump" because it is just that much easier.

Socializing your Brand

With the modern day market, people can sell and buy products from all over the world so there will be always be a consumer no matter what the product is. The hard part is marketing it to the right people and Branding your device so it becomes the best and baddest.
Look at all these brands. Its hard to imagine that people can probably name 50 brands than all 50 states of U.S. These products have embedded into our brains as the right product or only product. Anything else is sub par. They reserve the right to hike up their products just because they are on top. What is new though is the use of Social Media in Marketing strategies.

Social Media has become a tool to give emotion, feeling and thought to products and devices. People care about companies viewpoint on controversial issues and debates. People have even boycotted Chick Fil A for opposing gay right marriages.

It is imperative for companies to use social media now a days to bring fun and excitement to their product that does not correlate with anything to their actual product. Promoting a chance to win concert tickets when buying cereal and etc has become a common norm. The only way for people to hear about these things is through the social media. 

As simple as this sounds to make a facebook page, twitter account and/or youtube it does get confusing with all the media websites. In a easy world every single page would be connected together. The writers need be fair and unbiased because they need to appease the general public. Offending anyone would lead to disastrous results. The other problem with these websites is also the user security. Because most of them are made for the general public to use, most people do not know the security settings on the website.

It is imperative that no one else has claimed your Brand or name for themselves, also keep the logo in the front of the homepage and default icon. For companies it is generally useful to keep comments private so no distasteful comments are posted. Also any images posted must be protected so spoofs or parody's can not be made. At the moment there is no privacy on the online web. Anything posted to the public can be downloaded to one's hard drive. So companies need to make sure they have a filter process so nothing bad comes out.

Greetings fellow virtual entities

Hola.

This page contains my professional endeavor and experiences. I am a 4th year undergraduate student at SJSU. I invite you to roam through my page and offer creative criticism or plain negative criticism itself. My programming education ranges from familiarity with Java and C. I have decent network management skills for everyday installations and adjustments. My strength lies in utilities use and Android functions.

As a computer scientist I believe in the advancements towards the future. Nothing seems impossible with the rate of growth portrayed in our history. As a scientist not a programmer I want to test and prove theories that put people into disbelief. 

The most exciting part of this field is the history of it. Products and devices are never put to rest, instead they are reinnovated  and abused until it becomes the third part of a trilogy that producers create for more money. The past is always important, yet extremely boring. The really exciting part of history is whatever happens alters and effects the future.

-Do