Ivanlam27 - Bioinformatics (Level 2) Pathway

[ivanlam27]

Things that have learnt (Week 1):

Technical

Dissect the key features that were used in the Long et al., 2019’s paper, how they presented the quantitative data into visual representation
Criticise the paper and learn more about data presentation in good practice
Not many technical aspects involved for this week.

Soft skills

Collaborate with teammates, try to bring up the vibe as a project lead
Organise introductions and events, try to build up team spirits
TIme management

3 Achievement highlights of the week

• Understood more about the overview of this project
  – Debaleena have thoroughly described and explained the overview of this project through the leads meetings and gave a great insight into the direction of this project. Before that, I was a little bit confused with it and those meetings were very helpful to me.
• Build up teamwork
  – Try to connect with my teammates and work with my co-lead to sort out any issues in the team. Although sometimes was a bit awkward during the team meeting, we both managed to get through it.
• Prepare for next week tasks and set up a workplace for future tasks – Collaborate with project management lead to prepare for the future weeks’ tasks. It is basically a week for building up fundamentals before we dive deeper into this project.

[ivanlam27]

Things that have learnt (Week 2):

Technical

R: Spent some time learning some basic functions which could be implemented in the Rshiny app. Helping other interns with their basic R technical issues and trying to get everyone to the same pace and progress.

Rshiny: Started learning the basics structure of Rshiny, with the front end and back end structure and how they work. I was able to implement some of the simple functions into my designed app and it brings my interest in Rshiny further.

Github: I was able to set up my GitHub and repository on my end, as well as fork it into my repository. I also managed to create the repository for our group for later use. Thank you @Roman_Ramirez and @KellyZhang for giving those valuable ideas to me, who is very new to GitHub and was able to manage it at the end!

Soft skills

Bonding with teammates: As a leader, I tried to distributed everyone different from their partner from last week’s task (Journal Club) so that everyone could get to know more people by working with each other, but also expanding their connections and bonding concurrently. We are also planning to hold events after work to

Collaborate with others: @ashlesha.patil, lead of team 2, and I have tried to sort out the deliverables together. By working with other people, it is a great way to learn and gain from each other which I think is beneficial bidirectionally.

3 Achievement highlights of the week

• Understand the structure of the newly proposed optional project

By understanding it, I was able to explain this to my teammates, as well as gaining a better understanding of the overview of this project. This might be a very good opportunity to learn and gain more from the bioinformatics field. Besides, I would also like to support and work with others to create a final product for the showcase.

• Create my first Rshiny app

Although it was a very simple app, I was able to create something to present for the weekly meeting with the leads, which was a small milestone for me. I hope in the future weeks I will be able to create more useful functions and contribute to the creation of the final project.

• Worked ahead with my teammates

@veyssi and I were checking in with everyone and their progress in our team via Mon/Wed/Fri stand-ups and we decided to move a bit forward to module 3. I was also working with @Ananya_Kaushik and @Sharon2099 with this week’s deliverables and I have also learnt a lot from them, especially with the interpretation of plots, as well as coding which is the key of the deliverable.

[ivanlam27]

Things that have learnt (Week 3):

Technical

R: a week with slight intense coding and I’ve learnt a lot of new functions within the Bioconductor package, specifically with how to generate a volcano plot and finding the top differential expression gene (DEG) from a bunch of data (module 4). I was working with @Roman_Ramirez on these tasks and we will showcase them to the group next week.

Rshiny: After the introduction to Rshiny from the previous week, I have learnt more about the CSS and HTML code structure as well as specialising in the app layout field in the Rshiny project. I tried to get my head around these codes by adjusting them/recreate some of the components from the website and get myself familiar with building a good layout. I was mainly browsing around bs4Dash to learn more about UI in Rshiny and html.

besides the coding part, I have tried to jot down key features of the popular websites and how they designed their UI so that it’s easy to use.

Github: We sorted out GitHub and tried to get ourselves more familiar with how to use GitHub via asking everyone to upload their codes on GitHub, as well as splitting into groups to work so that within each group, we could have some experiences for working on Github.

Soft skills

Bonding with teammates: We held several socials this week and try to get everyone familiar with each other. Although the grouping has been changed recently, these were good opportunities for us to get to know each other more.

Evaluation: @KellyZhang has created a questionnaire for interns to fill in recently. Through having those comments provided by interns, these comments were able to reflect on our recent performance so that we can adjust our leadership and improve ourselves.

keep track of work: I have summed up and made checklists/lists of things for interns to work on after Monday’s meeting, with providing any useful information for interns such as guidances/instructions or other related pdfs if necessary, which was also reflecting onto the comments that we received last week.

Achievement/highlights of the week

• Try to get everyone up to the progress

We tried to work in an agile fashion and move on quickly with the easy tasks in the first few weeks/modules so that our team will have more spare time working on the more difficult tasks in later on modules since the workload might accelerate steeply.

• Learning from a new field

Layout and UI are totally new to me and there is still a lot for me to learn from everyone since I was mainly working on sorting data and other functional properties in R, but not in Rshiny. I was trying to step out of my comfort zone which might be very beneficial for my future.

[ivanlam27]

Things that have learnt (Week 4):

Technical

R: Our group have been successfully generated the Volcano plot for our data (original + outliers removed manually). From this module, I have gained more practical experience in sorting, selecting and fixing the data into formats. We are currently moving onto module 5.

Rshiny: I have started my LinkedIn learning course on Rshiny which gave me a very useful background of Rshiny with examples demonstrated, specifically creating dynamic UI with observeEvent(), upload and download files function which will be useful for the Rshiny project. Alongside LinkedIn learning, I have also used Mastering RShiny as an assist. These skills can be implemented when I am going to work with @Huikun_Li as a subgroup in Group B2 for the Rshiny project layout.

Soft skills

Novelty: I tried to explore new things in the field of R and Rshiny and tried out different platforms and see what can I get the most out of this internship.

Time management - agile kicks in: We understand that module 5 might be a bit overwhelming and we tried to split up the work as always. Since we also have spare time from the original timeline, we have decided that we should slow down the pace for this week so that everyone in the group could be more prepared. By doing so, we have put our weekly presentation and discussion forward from Tuesday to Thursday.

Achievement/highlights of the week

• Volcano plot

A plot for module 4, also a milestone for our data analysis and we start to be able to visually distinguish those outliers from a plot.

• First meeting for B2 layout team

Just had our first meeting within the B2 Rshiny project group and it is coming in a shape. I’m also very excited to work with Kelly on the statistical analysis layout page for this project!

[ivanlam27]

Things that have learnt (Week 5):

Technical

R: Getting more familiar with different functions in the Bioconductor package, AnnotationDbi and other general R functions. By working seamlessly with those function, it definitely boosted my efficiency during coding.

Here is the gene-oncology network diagram that @Leila and I worked out for this weeks’ deliverables. This also gave us a sense of which upregulated genes might have a detrimental contribution to the pathology.

Rshiny: first in touch with Figma, which allowed me to create and design the layout for the R shiny app. Here is our design with @Huikun_Li for the statistical analysis’s page layout.\

Soft skills

Communication: We have started communicating with the UX team for the Rshiny app design. It broadened my insight as well as knowing more about the field in UI/UX.

[ivanlam27]

Things that have learnt (Week 6):

Technical

web-tool: GEPIA - Gene Expression Profiling Interactive Analysis: this week’s deliverable has been moved from coding to using web-tool to further analysis the gene which has been identified from the previous module deliverables in Rstudio, and particularly, module 4 and 5, top 10 DEG and gene oncology network. @veyssi, @KellyZhang and I have worked on 3 different genes and run the survival analysis on GEPIA. I have chosen AGER for the analysis due to the highest fold change from module 5’s gene oncology network. Most specifically, we have targeted the correlation between the survival rate and the presence of the AGER.

Rshiny: I have uploaded the template code for the Rshiny app from bs4Dash, by David Granjon, and changed several variables and arguments. Here is a capture of the Rshiny app template layout snapshot:

Detail bullet points regarding technical skills from the Rshiny project:

• modify the template from bs4Dash by David Granjon
• use of ‘fresh’ package - changing pre-set colour from bs4Dash_color
• use of ‘bs4Dash’ alongside with ‘shiny’ package
• getting familiar with the functions in Rshiny: dashboardHeader(), dashboardBrand(), change colour theme with create_theme() + bs4Dash_color()

Soft skills

Communication: Communication between team members with accommodating their needs and providing clarification with the current progress

Organisation skill: Module deliverables has all been successfully accomplished. We will be moving onto the capstone project in the upcoming week. Organising the capstone project for team members who are willing to participate in this project.

Besides organising the capstone project, I have also tidied up the weekly discussion/presentation powerpoints and upload them onto the forum for future use or reference.

[ivanlam27]

Things that have learnt (Week 7):

Rshiny: Advance setting of Rshiny UI and industry-standard documentation and code organisation setting, as well as different customisation of the app with bs4Dash, HTML and CSS.
Beautification of the Rshiny app for next week’s showcase.

R: Applied the learnt skills from module deliverables in the previous weeks and pulled everything together as one. Modified codes in order to process different datasets from the GEO database.

Highlights

Capstone project:

Our group have started a capstone project on a different dataset: colorectal cancer, GSE4107, with @KellyZhang @Roman_Ramirez @Leila @Ananya_Kaushik. We have analysed this new dataset with the same skills applied in the module deliverables and we found that FOS might be a potential biomarker for the colorectal cancer from our statistical and functional analysis. This result is also synchronising with the current literature and a brief progress update has been attached with this post:

Progress for the capstone project: gse4107.pdf (2.2 MB)

Rshiny app layout:

Our Rshiny project group, group B2, have generated the first version of the layout.

This is the first layout that I have generated:

This layout has also been improved by @veyssi @Roman_Ramirez:

[ivanlam27]

Things that have learnt (Week 8):

Google slide: Created wrap-up capstone project presentation, utilising different presentation designing skills. Created a STEM-Away theme-related template for our presentation (see below for detail).

Rshiny: Modifying different layout functions’ parameters within bs4Dash, fixing bugs and reconstructed contact page by using HTML-related codes instead of HTML(). Implemented controlbar() with feedback form inside. Other miscellaneous such as implementing icons into the contact page.

Highlights

Capstone project:

Our group have successfully presented the capstone project and we also gained a lot of valuable feedbacks from @anya and Ali.
Presentation for capstone project:
Capstone project presentation.pdf (4.3 MB)
Here is also a screenshot at the end of the meeting:

Thank you @veyssi and @KellyZhang for the countless support throughout the time in Group 1, organising the meetings and tasks. Not to mention our powerful team @Ananya_Kaushik @Roman_Ramirez @Leila for making this presentation very interesting and fun, but also educational.

I would also like to thank everyone else from Group 1:RiceCRISPRTreats @aditi_3 @Shreya_Vora @sanisetti for your output to make this project and internship work seamlessly.

It was a fun time having you guys in the group and I think it really showed our teamwork gradually as we go along. I really enjoyed being a leader for this group and gave me an enormous experience, and DONT FORGET to put these Soft Skills and Technical Skills in your CV, as always!

Rshiny app:

B2 have given our internal presentation:

Thank you @veyssi and @Roman_Ramirez for the group management, with @Ananya_Kaushik support in order to make this happen.