New Insights on Chemistry and Technology: A Reflection

Important Lessons

Before participating in this course, I had minimal experience with the more technological aspects of chemistry. Through some of my other classes and research experiences, I had gained some knowledge with equipment or computational techniques, but not until this course was I so exposed to the progress that has been made in using computers to forward our knowledge of chemistry. I was aware of many of the advances made in chemical research in regards to chemistry itself, but I had no idea of the technological advances - for example, that 3D printers and AI/machine learning were completely changing the way chemistry can be researched and applied. I think it is absolutely incredible that as technology moves forward so quickly, some research that would normally take years of reading literature research and testing hypothesis can be streamlined through tandem work between computational and experimental chemists, in which computational researchers can narrow down hypotheses so experimental chemists can go into the lab with more knowledge and hopefully support what was found computationally. Not only does this tandem work save money, but it also supports the field of green chemistry in which researchers try to be less wasteful and safer for themselves and the environment.

Programming was never something that in my schooling prior to college or even in our general education requirements now that was emphasized specifically. My generation grew up with technology, so it was expected that we all had a basic understanding of how to use technology such as computers, smartphones, and programs - but knowing how to code was not an expectation, but a niche activity for those who enjoyed such activity or wanted a lucrative job. However, it is becoming more and more necessary for everyone to know how to code at least a little bit. It is incredible to know that now that President Obama has started and intiative so all students must gain exposure in coding sometime while in grades K-12 because it is an important skill to gain. This course has really shown me that coding is important and that it is a skill that can help me be more independent in my future - if I have an idea for a program that can help my research and I know how to code, I will not have to rely on someone else to develop for me, which is incredibly empowering.

I am still largely learning the different disciplines within my field and where distinctions fall, but I for the most part believed that computational and experimental chemists did collaborate, but were rarely the same people, prior to this class. Now I know that even those who work primarily in labs or in product testing still must be able to utilize databases and computer programs at the very least, which I learned mostly from my interview with a development chemist. I expected that I would get very little information from my interview with my chemist since they worked in development, but I was happily surprised to receive a lot of information from them, including how computers can help solve for needed reactions that would take very long for chemists to figure out without the help of a program. My interviewee also mentioned the use of spectrophotometers, which basic version I had used before in a lab setting, but it was quite interesting to hear how precise and advanced spectrophotometers could be with the help of computer software.

Figure 1. Computational models of molecules and proteins from PubChem database, including analysis of accuracy
(Kim, 2013).

Future Actions

This course has caused me to think critically about how aspects of technology impact chemistry and what I need to do to keep up with the changes in my field. I am considering taking a programming course sometime before I graduate - I had always been interested to learn but now I see that it is very crucial for me to acquire these skills. I would like to continue to learn how to utilize databases in part because, for chemistry, they are absolutely necessary tools with how much information is being acquired through research now. I also am currently considering becoming a research professor, so learning in this course how spreadsheets could be manipulated to make a personalized gradebook with code was something I did not know but could be useful in my future career. I hope to and will pursue more chances to work with computational researchers and equipment that require the use of computer software in the next few years so I can have a strong understanding of the complexities of such work and be able to troubleshoot issues better if I ever utilize such skills more regularly. On my own, I can look at journal articles such as those from the Journal of Cheminformatics to acquire new information about this growing field.

Resources:

Kim, S., Bolton, E. E., Bryant, S. H.  (2013). PubChem3D: conformer ensemble accuracy. Journal of Cheminformatics, 5(1).  10.1186/1758-2946-5-1.

Let's Talk About CSS and Google Analytics

The success of websites are crucial to any field. In chemistry specifically, websites that provide access to databases, journals, and products are necessary. Websites must be accessible to users as well, and look professional. The information given by a website could be correct, but if the website has different styles throughout and is hard to navigate, users will lose trust in the content quickly. CSS can help avoid formatting issues in HTML-based websites. It is also important for those who own the websites to be able to analyze who is visiting and other details of those visitors; Google Analytics offers a simple way to do this.

CSS

What is CSS?

CSS stands for Cascading Sheet Styles, and is a coding language that works along with HTML to allow websites to have consistent formatting across pages, as well as make professional presentation of content easier to achieve. CSS can format all text in factors like size, position, color, and other stylistic elements (Girl Develop It, n.d.).

How does CSS work?

CSS works in tandem with HTML in a few different ways. CSS can be utilized in a separate file known as a stylesheet that includes all the formatting data for the main HTML file that houses the content for the website, that are linked together (codecademy, n.d.). CSS can also be included directly in the HTML file, either as a separate style section or inline, though the separate style section is preferred since it deviates farther from standard HTML styling and is easier to use for larger projects (Girl Develop It, n.d.).

What is the CSS language made up of?

CSS uses rules, which are blocks of its code that include selectors and declarations, in which declarations are split into properties and values. Selectors can be for IDs or classes. IDs are reserved for single elements on a webpage, whereas classes are used for elements that are repeated. In the declaration - which comes after the selector - the property defines what will be formatted and the value declares what that formatting will look like (Girl Develop It, n.d.).

Example of CSS rule (Girl Develop It, n.d.).

Google Analytics

What is Google Analytics and how does it work?

Google Analytics is a service provided through Google that allows users to collect data from websites and mobile applications, as well as other digitally connected environments. Google Analytics is implemented differently depending on the digital source, but overall functions in the same way for each situation through a process that only starts with data collection. After raw data is collected, it goes through processing and configuration, and lastly, reporting (Google Analytics, 2013).

The process Google Analytics goes through (Google Analytics, 2013).

Collection

Collection is enabled through different coding techniques in different situations and systems. For websites, a small piece of JavaScript is embedded on each page to send data to Google Analytics' servers as a package known as a "hit" or "interaction" whenever someone visits that page. Some of the types of data that can be included in the "hit" are the browser the visitor is using to access the page, the country they are in as they access the page, and how long they stay on the page. For Blogger specifically - another Google service - only a tracking code must be added to the blog for Google Analytics to link to it and start collecting data. For mobile applications, JavaScript code pieces are not necessarily used, but a different method is used based on the operating system of the device. Data is then collected after an "activity" is completed rather than when someone has simply viewed the page. Data can also be collected when the device is offline and sent back when the device reconnects. Other digital environments can be linked with Google Analytics with similar but more complicated uses of coding (Google Analytics, 2013).

An example of a what Google Analytics looks like once a website has been linked, in this case, the Google Analytics linked to this blog.

Processing and Configuration

Processing is the step in which the raw data that has been sent back to Google Analytics' servers is organized and configuration settings used to process the data. Configuration settings will differ from user to user, and can allow the exclusion of data that may be useless. At the end of processing, data is stored into a database and cannot be changed. The database can then be accessed through the user's Google Analytics account and reports summarizing that processed data are also available there (Google Analytics, 2013).

Reporting: How Can Processed Data Be Analyzed?

Once a user has logged into their Google Analytics account, they can access the reporting interface and manipulate the processed data to utilize it for their needs. Many different aspects of the report can be changed to best analyze the data collected. The active data range can be changed, and also be compared to another date range across all graphs and reports. The main graph can also be changed to display by day, week, or month. Notes can be added to specific dates so the impact - or lack thereof - of events and campaigns can be measured. The metric displayed on the main graph can be changed and compared to another metric, the same way dates could be compared. Most reports also have tables where more data can be viewed and compared at once. Each row shows data for a different value of the dimension being analyzed, which could be country, browser, or something else entirely. The primary dimension is the dimension that will be shown in the first column, while a secondary dimension can be added into the second column so data can be refined. For example, the amount of users from the same country using the same browser to access a page can be analyzed using the country and browser dimensions together. The search feature allows only relevant data to be shown based on a search value. The advanced filter can be used to shown more specific data, which is quite useful when trying to remove sets of data that are so small that they are insignificant. There are a few different view options for reports, which include data view - shows tables, percentage view - shows pie charts, performance view - shows bar graphs, and comparison view - to see how different values are doing against each other. Specific segments of the data table can be viewed on the main graph and compared using the Plot Row feature (Google Analytics, 2013).

To show how useful CSS can be, this blog post was actually made using HTML and CSS instead of Blogger's ready-to-go blog composer.

Resources:

codecademy. (n.d.) CSS: An Overview. [Online Lesson]. Retrieved from: https://www.codecademy.com/en/courses/web-beginner-en-TlhFi/0/1?curriculum_id=50579fb998b470000202dc8b

Girl Develop It. (n.d.) Intro to HTML/CSS. [Slides]. Retrieved from: http://girldevelopit.github.io/gdi-core-html-css/class2.html#/

Google Analytics. (2013, Oct. 31) Digital Analytics Fundamentals - Lesson 3.1 How Google Analytics Works. [Video file]. Retrieved from: https://www.youtube.com/watch?v=eyltEFyZ678

Google Analytics. (2013, Oct. 15) Digital Analytics Fundamentals - Lesson 5.1 Reporting overview. [Video file]. Retrieved from: https://www.youtube.com/watch?v=xyh8iG5mRIs

Intelligent Molecules: Applications of Machine Learning in Chemistry

Machine learning is an aspect of computing that falls under artificial intelligence that allows information to be collected, digested, and used in the future. There are two types of machine learning: supervised and unsupervised, which differ in if the answer that we will get is known or not already.  Machine learning is used primarily in computers and online systems to save preferences and tailor the experience to the human user. In those application, the “machine” acts as if it has a brain and remembers information so it can regurgitate it later in a situation in which it would make sense, as people do in conversations.

However, not all applications of artificial intelligence must be in computers or online systems. Computer scientists and biological engineers at Harvard have been trying to apply machine learning to molecules that could eventually “that can automatically detect, diagnose, and treat a variety of diseases using a cocktail of chemicals.”

The mathematics and biology necessary to input machine learning into molecules.

Nanotechnology has become a larger focus more recently, so it would be reasonable for the next step in machine learning to move from the macroscopic to the microscopic level, and to biological systems. Currently,  therapeutics do not change in response to the body, they only carry out their predetermined task. If drugs could respond to the body, human error in diagnosis and treatments would be reduced. In research, molecules would be able to relay better data would be able to be collected and characterized better than chemical reactions can be now, since it is difficult to study reactions in situ.

In the future, I believe machine learning implemented in molecules could revolutionize therapeutics for mental illnesses such as bipolar disorder, which changes more frequently than other mood disorders such as depression. Researchers could always use extra help, why not have the molecules and biological systems they are studying do just that?

More biologically and chemically relevant applications of technology can be found at the Wyss Institute which contributed biological engineers to the project of implementing machine learning into molecules.

Sources:

Article: Perry, C. (2013). Programming smart molecules. Harvard.

Picture: Napp, N., Adams, R. P. (2013). Message Passing Inference Networks with Chemical Reaction Networks. NIPS Proceedings, 1-9. https://www.seas.harvard.edu/news/2013/12/programming-smart-molecules

Interview with a Professional Development Chemist

I was lucky enough to interview a development chemist this week. Jordan Wilkins* focuses on the DOE - design of experiment - to provide the exact colors of paints that their clients want, for industrial purposes. However, providing the correct color in a reliable and lasting paint is not a simple task. Paints are based on resins, which are organic molecules that come from plants and other natural materials and often need to be switched out to fit specific needs. Other compounds are also used to achieve the wanted results such as silica, iron (III) oxide - which is used for pigment - and xylene - which is used as a solvent for some paints. It is likely that you have experienced xylene before in your everyday life, as it is what is used in some permanent markers and makes their distinct smell.

iron (III) oxide (1)

silica (2)

xylene

different isomers of xylene

A balance of hydroxides and hydrogen ions must be kept to maintain the proper pH for the paint to work. The paints must also be suited to the conditions in which they will be used. As paint dries, a reaction is occurring aided by catalysts, in which the reaction must complete at the same pace as the catalyst. 

It can be a long and complicated process to figure out what reactions must occur to develop the wanted product, but technology can help developers like Wilkins with the process. One of the main pieces of technology used in paint development are computer programs that, when given an input of a desired product based on color and conditions, will give an output of many reaction options that will likely work to reach that product. These computer programs are known as formulation tools, and also assist in figuring out how to balance hydroxide and hydrogen ions, in narrowing down which of the output reactions are more realistic for the purpose given, which resins to switch to, as well the reaction rates present and needed. Every time a change is made to the reaction process, that change can be input into the programs so a sample tree can be developed and the programs will determine if the change is substantial. An example of this would be if the temperature of a reaction is changed, sometimes that change is not drastic enough to actually modify the reaction because most reactions can happen under a range of temperatures, not just one singular temperature. Once Wilkins knows what reactions might work, they can run large batches of reactions and continue to give the computer programs more input so they can continue to help Wilkins narrow down their options.

The formulation tools involve the use of on-site databases that are private to their company, which currently are based on spreadsheets. Sometimes, Wilkins and their fellow research chemists must go in and edit the spreadsheets to get the results they need, and as a way to upgrade their system. In the future, the databases will be moving into web-based systems by another department at Wilkins' company so they will not have to use code to develop it. However, Wilkins and other employees at the company will be able to use the databases on any company-approved device through that device's web browser, which will include mobile technologies. The main benefit of having mobile access to the databases is that the employees that visit customers and receive specific questions about their paint can use those databases on-site instead of having to call the employees that are back on computers within the company's system. The only outside databases that Wilkins' company uses are industry standards for necessary information.

Once Wilkins has developed a new paint sample, a spectrophotometer can be used to test that the color the customer has asked for was made. Spectrophotometers are a very standard piece of technology used by chemists at all levels, as they vary in complexity and applications. Spectrophotometers generally work by sending light to a sample to test absorption of certain wavelengths. For industrial purposes, a spectrophotometer that is able to read metallic colors must be used, since industrial paints will dry to produce films that have both shine and pigment qualities that will change under different angles and light effects on their metal surfaces.

example spectrophotometer for metallic colors (3)

how metallic paints will react with light to produce

their color and shine once it has dried to its surface (4)

Though spectrophotometers can provide readings on screen, the data usually needs to be furthered analyzed using a software program on a separate computer system. An example software program is developed by Cyberchrome, whose's products can be found at their website: http://www.cyberchromeusa.com/products.



*Name changed to protect privacy. The interview responses reflect only the opinion of the interviewee, and not the formal position of their unnamed company or the industry they work in.

Chemical structures were made with ChemDraw.

References:
1. https://en.wikipedia.org/wiki/Iron%28III%29_oxide#/media/File:Iron%28III%29-oxide-sample.jpg
2. http://www.chm.bris.ac.uk/motm/silica/silicah.htm
3. https://www.byk.com/en/instruments/products/?a=2&b=18&f=0&faction=#fam1
4. http://blog.xrite.com/using-spectros-for-print-packaging-manufacturing/

Opinions of Databases and Cheminformatics in Pharmaceutical Research

This week, a survey was sent out to thirteen people (eleven university students, one post grad and one family member) who had agreed to take the survey after a short private correspondence. At the cut off time for the survey, nine of these people had responded. From this point on, those people will be referred to as respondents. The survey overall focused on the opinions people have on databases and cheminformatics in pharmaceutical research.

Original Survey Link (click to view)

The first question asked for this survey was “How would you describe your knowledge of and/or interest in chemistry?” to gauge the respondents for later questions, since pharmaceutical research is largely based in chemistry. Five of the respondents saw themselves as having a high interest/knowledge base in chemistry, whereas three respondents viewed themselves as moderate, and one respondent viewed themselves as neutral. No respondents chose Very High, Low, or Very Low. Most respondents were determined to have a fair basis to reasonably complete the rest of this survey with enough understanding of the topics discussed.

The second question asked respondents to comment on the importance of all pharmaceutical researchers to understand how to apply databases to their research. Seven respondents said definitively that all pharmaceutical researchers should understand how to utilize databases, and two respondents said “probably.”

For the third question, the focus was on how skilled pharmaceutical researchers that do use databases should be in the actual mechanisms of databases. This question had the largest split in responses, with all four options being chosen by at least one of the respondents. People do not agree on if pharmaceutical researchers need to be able to construct databases or just use them - this split could have been influenced by the field of the respondents and how heavily their chosen field is focused in chemistry and technology.  Four respondents thought that researchers should generally understand how databases work, whereas one respondent thought researchers should be so strong in databases that they could develop one of their own - on the other side, three respondents thought that researchers could pursue more knowledge on databases but do not need to, whereas one respondent thought that the researchers should focus on utilizing the databases more than understanding them.

The fourth question asked for open ended answers from the respondents on what purposes researchers may need to have coding skills for. Some common responses had to do with coding for databases and websites. A very specific example was to simulate drug design and help patients through computing; another response talked more generally about using the computer to model aspects of chemistry and biology. 

The fifth and last question asked if undergraduate students with an interest in pharmaceutical research should gain a strong level of understanding of databases and cheminformatics now or later. Answers ranged from maybe to yes, so all respondents thought at the very least that it could not hurt to begin to understand these aspects of computing.

It is also highly likely that the information provided throughout the survey assisted in gaps of knowledge the respondents may have had, because of the specificity of this survey and the technicality of this field.

These results show that respondents do believe that databases are important, especially for pharmaceutical researchers. Databases are quite expensive, and it is not clear from this survey if respondents were aware of this or not. However, most databases are funded by the government and used by so many people around the world that the cost is worth it - especially since pharmaceutical research focuses on bettering the health of people who need it. Most respondents did not think that pharmaceutical researchers need to be well versed in how to make and upkeep databases, or be able to code, though the respondents provided reasons the researchers could if they chose. Most database management is likely performed by computer scientists and not by the researchers who utilize the databases anyways, so it is not necessary for those researchers to understand the mechanisms of the databases, though it could be helpful. It is important to note that the databases that researchers are using are likely supervised, because the researchers would know what information they are looking for - this changes how those running and using the databases interact with them.

What does this mean for the future? It would definitely be helpful if undergraduate students studying chemistry receive exposure to databases and how they work during their coursework, and if all pharmaceutical researchers understood how to utilize databases in their research, even if they do not use them frequently.

Technological Advances in Pharmacology: 3D Chemical Printers

Drug discovery and design are large areas of research within chemistry. Most drug research must be conducted by highly trained organic chemists or biochemists, however, the processes are very time consuming and inaccessible to the general public who need such medicine. For most drugs, the general public must wait through a long process in which researchers design and test drugs, the FDA must approve new drugs, and then finally pharmaceutical companies can produce the drugs for sale. Regardless, the general public must go to a medical doctor for a prescription before they can even receive the produced drugs, but what if there was a way for those patients to go home with algorithms instead of prescriptions and make their own, personalized drugs? Research professor Lee Cronin hopes that this can be the future, and has been working since 2012 to research a way for people to “print their own medicine,” as he describes in the TED video below.

Cronin and his team have been working on developing a 3D printer that can print chemicals and reaction chambers. 3D chemical printers would also be equipped with testing devices so reaction progress could be monitored on computers analyzing the data from the testing devices. As of now, 3D chemical printers are of most use to pharmaceutical companies such as Aprecia Pharmaceuticals, a company that developed the drug Spritam through 3D printing methods. Spritam is easily dissolved with just a sip of water because the 3D printing methods allow it to be made to work with "Zip-Dose Technology," meaning that the drug is very porous. The high solubility of Spritam adds a benefit to this new drug production method as it allows consumers to more easily take their pills. The purpose of Spritam is to treat epileptic seizures, and it was just approved by the FDA in 2015.

Right now, it is not possible for people to have 3D chemical printers in their home. However, in just three years from the start of research there has been enough progress for an FDA approved 3D printed drug to exist. The more companies like Aprecia Pharmaceuticals and researchers like Cronin continue to work on these technologies, the more advances will be made. Once the technology becomes cheap and secure enough, is will be possible for 3D chemical printers to be as common as home computers and laptops. In the meantime, synthetic chemical researchers can use the printers for their research, as can pharmaceutical companies. It is also likely that pharmacies may be able to use printers on site, especially since pharmacists have vast training in chemistry that would allow them to quickly understanding the technology and ways to use it.

References:

TED talk: Print Your Own Medicine

Lee Cronin and His Research Team

The Guardian: Lee Cronin and "Chemputers"

Washington Post: FDA Approval of Spritam

Aprecia Pharmaceuticals Website

Spritam Picture