Category Archives: Outreach Project

Programming by Optimization

In today’s increasingly computer-oriented world, the development of software must also keep up with achieving certain tasks to meet demands. During the creation of such software, however, developers often explore different methods or paths in order to achieve a desired task. A problem that often arises though is that during the development of this “desired task”, alternate solutions that are thought to be nearly impossible to use gets thrown away, when in reality these methods might have worked later on.

Fortunately, Dr. Holger Hoos along with his research team at the University of British Columbia are working on introducing a type of design called Programming by Optimization (PbO) that directly prevents this premature toss of solutions. This has been proved to be incredibly beneficial to the development of software and leads to huge increases in software efficiency.

This is excellent news for the computer world as one of the biggest goals of large companies is increasing processing speeds and reducing running costs by, for example, using better organizational and scheduling procedures. This is where PbO shines!

PbO allows users to locate mistakes that weren’t noticed at first – this is the debugging process. PbO debugs all problems of each step in creating software separately by using interchangeable codes and provides a more efficient way of finding the correct problem. Dr. Hoos and his research team have already found a bug in a widely used commercial software using PbO and the company expressed their gratitude for it.

Although PbO is still in the research process, it has gathered a lot of attention from major companies around the world. Among others, Google showed great interest in PbO and the research team is currently working with IBM as well.

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A component of PbO that makes it so amazing and attractive to companies is its flexibility and adaptability to software and data centers. The video above mentioned university exam timetabling as an example. Since exam periods involve many students and courses, it is very difficult to put together exam times that fit every student’s schedule. This is complicated further with the limited number of rooms available during an exam period that only lasts a couple weeks.

Now, if we were to compare the Spring semester to say, the Summer semester, you can imagine that each semester will have entirely new courses. With PbO, the scheduling of these diverse timetables comes at ease. This also works across universities, so optimization can generalize the different situations so that it can be applied to scheduling at UBC Vancouver as well as UBC Okanagan.

Data center. Image by The Ark.

The following podcast is a short talk by Dr. Hoos explaining how PbO can help data centers run better:

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As more and more software get developed, programmers need a general plan to guide them through the designing process, so we can all continue to benefit from the efficiency and creativity that optimized software bring to us everyday.

References & further reading:

Hoos, H. 2012. Programming by Optimization. Magazine Communications of the ACM, 55(2). http://cacm.acm.org/magazines/2012/2/145402-programming-by-optimization/fulltext

Could the new Cyclosporin be in our own bodies?

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The Immune system Simplified (Nobel Media)

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Recent research at the BC children’s hospital in Vancouver, Canada has unearthed one of the mysteries of an immune cell that may play a key role in combating auto-immune diseases.

"A Regulatory T Cell" Image Source: http://www.iayork.com/Images/2008/12-8-08/BioLegendTReg.png

The cell in question is the regulatory T cell (Treg), a regulatory cell responsible for the management of immune responses. While largely unstudied, this cell has been found to prevent disease and illness brought on by the body’s own immune system. Tregs monitor our immune systems and counter-balance the constant assault against the cells within our bodies both malignant and benign. In a sense, they’re the whistle blowers of the body police.

While the job of Tregs is to control and reduce immune response, they can also be used to quell a person’s runaway immune system and subdue the illnesses our immune systems can sometimes create.

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While Treg therapy may seem futuristically out of reach or too good to be true, preliminary trials so far demonstrated promising results in human and mouse models. Anti-immune therapies using Tregs have been so effective and versatile that they not only treat the inflammation in Crohn’s Disease but tissue rejection in organ transplants. At times, this cell is  even capable of giving the body life long tolerance to the transplanted foreign organs.

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"Simplified Illustration of the Inflammatory Response" Image Source: http://www.rkm.com.au/immunology/immune-images/IMMUNE-inflammation-R-600.jpg

Despite these triumphs, Treg therapies still have a long way to go. The recent discovery found by the BC researchers shed light on interactions of Tregs with Neutrophils, immune cells involved in the generic first response of immune systems. While Tregs are meant to suppress immune responses, they seem to attract neutrophils in vast quantities which are highly inflammatory in nature. Until more is known about the relationships and functions of Tregs, researchers may run the risk of accidentally triggering an immune response when trying to reduce it. Another possible risk to consider is that Treg therapy may increase our risk of cancer by suppressing the cells responsible for keeping it in check.

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Despite these risks it is obvious that Treg therapies have an untapped potential with almost limitless application to illnesses associated with an overactive immune system. Our bodies’ tolerance of Tregs and their adaptive and responsive nature make them not only ideal in that they act like living cyclosporine, but they have been tweaked and perfected to be the ideal  immune suppressant for over millennia, before we ever got sick.

 

 

 

The Haber process

The Haber process is the nitrogen fixation reaction of nitrogen gas and hydrogen gas using an iron or ruthenium catalyst, under high temperature of 500c and pressure of 250 atmospheres (Clark 2002). The goal of the process is to convert nitrogen and hydrogen from the atmosphere to ammonia (NH3). Ammonia is very important to fertilizer industry.  Approximately 80% of ammonia is used as fertilizers and it helps provide increased yield of crops (Clark 2002). One of the top challenges for organometallic chemistry is to find a way to catalytically produce ammonia from nitrogen at room temperature and ambient pressure.

Although nitrogen gas makes up 78% of Earth’s atmosphere, it is chemically unreactive under normal condition due to the triple bond between two nitrogen atoms. High energy is needed to break these bonds (Ausetute 2012). Nitrogen fixation occurring in plants is slow. With the help of the Haber process, nearly 100 million tons of ammonia fertilizer is produced every year, yielding taller and healthier crops.

N2 (g) + 3 H2 (g) ⇌ 2 NH3 (g)   (ΔH = −92.22 kJ*mol−1)

The production of ammonia is exothermic. There are 4 molecules on the left-hand side and only 2 on the right-hand side. The reaction is reversible and will reach equilibrium when the rate of forward reaction equals the rate of reverse reaction.

If we increase the pressure the system will favour the reaction, producing more ammonia. This is Le Chatelier’s Principle. To get more ammonia produced, high pressure, i.e. 250 atmospheres is needed. Increasing the pressure also speeds the reaction. Under high pressure, molecules are brought closely together and able to contact with the surface of the catalyst. The higher the pressure, the faster the rate of a gas reaction will be.

The catalyst, on the other hand, does not play a role in the position of chemical equilibrium. It lowers activation energy and hence increases the reaction rate. Osmium and ruthenium were used as catalysts at first and iron catalyst is used more often now (Ausetute 2012). Iron is more active so less pressure is needed.

In UBC, Dr. Martinez and her research group are trying to find a way to obtain hydrogen and nitrogen from air and make ammonia without consuming too much energy.

Our video, discussing nitrogen, ammonia, the Haber process and its impact on the fertilizer industry.

https://www.youtube.com/watch?v=T6S02rwVUp8&feature=player_embedded

Our podcast. A brief overview of the environmental impact of the use and production of  nitrogen fertilizers.

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References:

Clark,J. 2002. http://www.chemguide.co.uk/physical/equilibria/haber.html (accessed Apr.  1 2012)

Asecute. 2012. http://www.ausetute.com.au/haberpro.html (accessed Apr. 1 2012)

Pictures:

http://www.nasdaqinsurance.com/wp-content/uploads/2011/07/crops-insurance.jpg

 

Video creation tutorials

As you start thinking about your video and podcast projects, I thought I would post a couple tutorials about making videos from the Vimeo Video School. There are a lot more to be found if you follow the link, but here are a couple embedded right here on the blog that I think I particularly important. The first one includes some shooting basics and the second one discusses general video editing.

Video 101: Editing Basics from Vimeo Staff on Vimeo.

Depending on which piece of software you are using for the editing, you can watch a more detailed video about using Microsoft Movie Maker (on a PC) or iMovie (on a Mac).

It seems to be a little more advanced, but Lifehacker also has a series of tutorials about video editing.

Finally, there is also a page on the UBC Wiki about video production that includes tutorials and a whole bunch of links to other resources.

Happy shooting!