BIOL368/F16:Class Journal Week 15

Isai Lopez

1. What is the most important thing that you learned this semester in this class?
   • With your head (biological or bioinformatics principles)
     • I learned a lot of information about the principle proteins responsible for making HIV-1 such a difficult virus to treat and target. Later on in the semester, in my Immunology course, the topic of HIV-1 came about and we discussed in class how the virus evades the immune system as well as how the virus replicates and eventually overwhelms the host's immune system. From the papers we read in class, the topic became much more clear and easy to understand.
   • With your heart (personal qualities and teamwork qualities that make things work or not work)?
     • I learned that one of the primary qualities in making a strong group member is the ability to communicate effectively in terms of what parts of the assignment each member is assigned to. The project was streamlined incredibly well because each group member was tasked with a specific section and we all completed them in a timely manner, utilizing our time to the best of our ability.
   • With your hands (technical skills)?
     • One of my favorite programs we learned to use this semester was the Cn3d program, in which we were able to create a 3D model of a protein structure and analyze each part of the structure (primary, secondary, tertiary, quaternary) and highlight specific residues for later analysis.
   • What will you take away from this class that you will still use a year from now?
     • The practice we got in reading dense biology papers was very helpful in learning how to break down complicated tables and figures to more understandable language.

• Isai Lopez 02:00, 13 December 2016 (EST):

Colin Wikholm

1. What is the most important thing that you learned this semester in this class?
   • With your head (biological or bioinformatics principles)
     • Learning about HIV-1 from the DNA level to protein structure level was really valuable to my understanding of infectious disease and microbiology. Not only did I learn about a very impact disease, I was able to make connections to other topics such as Cystic Fibrosis (especially evasion of host immunity). I believe that the concepts I have learned in this regard will contribute greatly to my continuing education in biology and, eventually, medicine.
   • With your heart (personal qualities and teamwork qualities that make things work or not work)?
     • I learned that it is imperative to have strong team members who are willing to actively contribute their time and effort. Intelligence and natural talent are nice, but lack of effort is by far one of the worst qualities one have in a team member. Such actions are inefficient and places extra work and stress on the individual who has to makeup for the deficit. I mentioned similar ideas earlier in the year, and they have only become reinforced since then.
   • With your hands (technical skills)?
     • I think the most important technical skills I learned this year was better modes of accessing, investigating, and analyzing scientific literature. I also learned about various databases and how to better navigate them. I will likely continue using these skills for the rest of my life (especially professional life), and am grateful to have improved relevant skills this semester.
2. What will you take away from this class that you will still use a year from now?
   • A year from now, I think I will probably still use many of the reading and critical analysis skills I learned in this class. Examples include not being afraid to question the author (or experimental procedure), and have the confidence to disagree with what is being stated.

Colin Wikholm 00:24, 13 December 2016 (EST)

Will Fuchs

• What is the most important thing that you learned this semester in this class?
  • With your head (biological or bioinformatics principles)
    • That there is often more than one answer to questions its only a matter of evidence collected that can show us the right direction. Trends and correlations are the closest things we can get to absolute truth. The amount of work that goes into explaining seemingly simply phenomena is astounding and I have a new respect for Bioinformatics.
  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • I've learned to be a little less anxious about group assignments and that I can rely on my team more too get through difficult areas of work. I've gotten over that apprehension that I must rely on myself more than the group.
  • With your hands (technical skills)?
    • The different statistical analyses that I've used in this class and to more masterfully navigate excel. It was also rewarding to be able to use Biology Workbench now.
• What will you take away from this class that you will still use a year from now?
  • Definitely the teamwork and presentation skills that I've had numerous opportunities to exercise.

William P Fuchs 21:58, 12 December 2016 (EST).

Matthew Allegretti

• What is the most important thing that you learned this semester in this class?
  • With your head (biological or bioinformatics principles)
    • I learned a great deal about the function and structure of HIV and how it affects those it infects. I also learned much about how it could potentially be treated as well as the prevailing thoughts on how it may eventually be cured.
  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • I learned that communication is essential, especially when meeting with your partner is not always easy. Also, it is essential to structure a project early so that it is possible to coordinate its completion without needing to meet with all members of the group to assign tasks.
  • With your hands (technical skills)?
    • I learned a but of wiki syntax. I also learned how to use a variety of bioinformatics tools such as the Biology workbench. I can now easily align and analyze both DNA and Amino Acid sequences in order to examine how changes within them leads to overall changes within the organism they came from.
• What will you take away from this class that you will still use a year from now?
  • Learning the various statistical methods in the last portion of this class will remain useful throughout my time in the field of science, especially when working with large data sets. Also, general knowledge of HIV may still be useful in the future, even if it is only to explain to others how the virus works.

Matthew R Allegretti 18:32, 11 December 2016 (EST)

Shivum Desai

• What is the most important thing that you learned this semester in this class?
  • With your head (biological or bioinformatics principles)

    • I learned how to look at biology from a information standpoint instead of simple a molecular view. It is difficult to understand that new research can still be found by using information compiled in database and that simply analyzing this information in different ways can allow for those breakthroughs.

  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • Due to the many group presentations required by this class, I learned how to evaluate group members quickly at the beginning of a project, how to assign tasks if need be, and what role to take within the group, earlier on instead of waiting until the end.
  • With your hands (technical skills)?
    • I learned how to format syntax on websites like wikipedia and openwetware. This is something I never knew how to do before. I didn't even know it was a concept.
• What will you take away from this class that you will still use a year from now?
  • I will now understand that there is always different ways to look at biological data as well as tools that can be used to analyze data in ways that is very specific to biology. Most likely I will not use this information again, simply because I am not very interested in data analysis or biological research, however if the situation arises in which I do need to perform the analysis of biological data, then at least i will know how to do that.
• Shivum A Desai 16:39, 11 December 2016 (EST):

Matthew K. Oki

• What is the most important thing that you learned this semester in this class?
  • With your head (biological or bioinformatics principles)
    • I learned to read articles and journals with an open mind, but don't be afraid to critique the paper. Everyone makes mistakes, and just because the research is published does not mean that everything will be perfect with the project or article. I also learned about certain research about HIV being conducted currently. It was interesting to analyze data on such a prominent and pertinent topic.
  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • Teamwork is a crucial part of presentations. I learned to divide work evenly among each team member, and also listen to each group member's input. Everyone's ideas can contribute to the overall project, and every idea is helpful in some way or another. I also feel like I learned to be a better group member by actively looking for something to do on the project, and not waiting until the last minute to complete my part.
  • With your hands (technical skills)?
    • I learned how to wikisyntax, and how to use certain bionformatic programs to interpret different types of data. I also learned a different way of formatting powerpoint presentations to have more explanatory titles and specific syntax.
• What will you take away from this class that you will still use a year from now?
  • The main takeaway from this class for myself will be the analysis of data and articles. I can analyze different types of data with the assistance of computers and programs. This will allow me to diversify the types of results I can get, as well as what data I can interpret to begin with. I also realize how to analyze articles more efficiently and more in depth. I don't take everything for fact in all of these articles for a majority of reasons learned in this class.
• Matthew K. Oki 21:56, 12 December 2016 (EST):

Courtney Merriam

1. What is the most important thing that you learned this semester in this class?
   1. With your head (biological or bioinformatics principles)
      • How to properly use and understand biological databases.
   2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
      • How to collaborate with partners while now working together in person (Thankyou google docs)
   3. With your hands (technical skills)?
      • How to write in wiki syntax and remembering to save often
2. What will you take away from this class that you will still use a year from now?
   • Properly citing all my resources for every assignment

Courtney L. Merriam 20:58, 6 December 2016 (EST):

Zach Goldstein

What is the most important thing that you learned this semester in this class?

1. With your head (biological or bioinformatics principles)
   • This semester I learned that just because a paper is published in a well respected journal does not mean we can accept it as perfectly accurate and true. I learned that, as scientists, we have to always question and look to refute what is accepted by the majority because there are often biases in poor research practices and the information that is conveyed through a paper or scientific journal. I learned the importance of understanding methods and background, and not just results, because through these aspects of a paper you can criticize published work and run experiments of your own to disprove them. I also learned how to navigate through numerous databases and realized how much information is out on the internet if you know the right place to look (or can afford access).
2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
   • This class made me realize I cannot do all projects on my own. Normally when I am assigned to a group project I like to do most of the work myself, but analyzing and presenting on these papers has shown me sometimes that is just not possible. Teamwork is very important in this class, and you have to learn to trust your partners like you trust yourself.
3. With your hands (technical skills)?
   • I learned how to use databases to search for information and run nucleic acid and amino acid sequence alignments, highlight differences, and create rooted and unrooted phylogenetic trees. I also learned how to write in wiki syntax which is a fun skill to have, although i don't know how practical it will be for my future classes or projects.
4. What will you take away from this class that you will still use a year from now?
   • From this class I will take a much clearer understanding of what bioinformatics is and how it plays a huge role in connecting emerging fields of biology.

Zachary T. Goldstein 21:10, 8 December 2016 (EST)Zachary T. Goldstein

Jordan T. Detamore

What is the most important thing that you learned this semester in this class?

1. With your head (biological or bioinformatics principles)
   • I learned how to thoroughly read studies and work out areas where I have confusion in order to fully understand the processes and results of the study.
2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
   • I learned how to break up projects effectively so that nobody feels like they are doing more work than the other and the projects comes together smoothly
3. With your hands (technical skills)?
   • I learned how to use wiki and also a great variety of analysis programs including biology workbench and STEM
4. What will you take away from this class that you will still use a year from now?
   • I will probably take away the research skills that I learned in this class more than anything. I also feel like this is the most important skill that I learned as it is applicable to a variety of different subjects.

Mia Huddleston

What is the most important thing that you learned this semester in this class?

1. With your head (biological or bioinformatics principles)
   • The most important thing that I learned this semester was that even if a paper or journal is published, it may not be completely credible. I learned that it is important to always look critically at each source you find. From this I have also realized how much goes into any research project and that the people behind each research project are only human.
2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
   • I have realized how important it is to trust your team members and especially how important it is to meet in person with those team members to know that you are on the same page.
3. With your hands (technical skills)?
   • I have learned so many technical and bioinformatics skills that I will happily put on my resume. I have also learned a lot about research and how important it is to document every step of the way.
4. What will you take away from this class that you will still use a year from now?
   • A year from now I will remember how you must put as much work into something as you want out of it. I have spent a lot of time in this class and I feel that I have learned a lot from it.

Mia Huddleston 19:13, 12 December 2016 (EST)

Anindita Varshneya

• What is the most important thing that you learned this semester in this class?
  • With your head (biological or bioinformatics principles)
    • I learned about different aspects of bioinfomatic analysis, especially in regards to HIV. Learning about HIV in all its from its viral mechanism through its protein structure helped my ability to analyze all aspects of biological information. I also learned about the importance of reproducible research in the scientific community to produce reliable data.
  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • Communication is essential for a group to work together. If group members do not actively participate in discussions about the group project, the project will not benefit from all of their knowledge bases. Furthermore, it is important for group members to help teach each other different aspects of the project that they may have mastered while completing their own part of that project.
  • With your hands (technical skills)?
    • Biology Workbench has many uses outside of this class, and learning to use the program could quite possibly come into use in the future. Furthermore, I learned quite a bit about analyzing protein structures using Cn3D.
• What will you take away from this class that you will still use a year from now?
  • I will definitely use the lessons I learned from working in group projects in the future. Furthermore, I appreciated the practice reading complicated journal articles. I feel that analyzing and understanding articles outside of my area of expertise will greatly benefit my educational growth in the future.

--Anindita Varshneya 01:55, 13 December 2016 (EST)

Avery Vernon-Moore

1. What is the most important thing that you learned this semester in this class?
   • With your head (biological or bioinformatics principles)
     • I think I learned mostly about HIV-1 and specific processes of it. I learned how to better analyze data and use bioinformatic tools to do so. This class increased my understanding of research, presentations, technology and using databases.
   • With your heart (personal qualities and teamwork qualities that make things work or not work)?
     • I made some great friends in the class, and I think that was an important aspect of the class. I learned to collaborate and work with these people, but gained some friendships out of it. I would say communication was a big part of working with others and making sure everybody was involved.
   • With your hands (technical skills)?
     • Learning how to use openwetware, biology workbench, and even excel all were tools I learned how to use technically.
   • What will you take away from this class that you will still use a year from now?
     • For me personally I will take away that I am capable of understanding and analyzing any research, whether the paper seems beyond my knowledge or not. Through our journal club presentations I always went into thinking I was not going to be able to understand the topic, and always came out of it with a much higher understanding of the material. Learning how to read the papers and go through them will help me in the long run.

Avery Vernon-Moore 21:31, 13 December 2016 (EST)