Bioinformatics teams are getting ready to start!

I am releasing this self-assessment earlier than planned. It includes questions on R, Git and Asana.

You will still work on a pipeline next week (the 1st steps for the July project) but we are excluding the pipeline from your self-assessment.

Please continue using office hours to help ramp up for the session!




This topic has been created to give you a birds eye view of all events related to Bioinformatics.
Please refer to July 2020 Calendar for event details and any last minute changes.


Notes


  • Self -assessment: Implementation of a simple Bioinformatics pipeline using R libraries. Pipeline specifications will be uploaded to drive. Questions on Git, Asana
  • Deadline: 07/17
  • Get all the help you need from the office hours below.

Learning Resources


Office Hours


Title: Basic Programming in R by Anya
When: Monday, July 6 at 9:00 AM PDT
Details: Please download R and RStudio and be familiar with concepts in the R training video from 6/02 before you come.



Title: PCA plots, Importing/Exporting Data, and an Introduction in R by Medhini
When: Tuesday, July 7 at 10:00 AM PDT
Details: Please download R and R Studio before coming and watch the 6/2 and 6/5 R Training videos!



Title: STEM-Away Forums & Slack by Kristen
When: Tuesday, July 7 & 14 at 9:00 AM PDT
Details: Just bring yourself and questions!



Title: Troubleshooting in R, Q&A by Alicia
When: Wednesday, July 8 at 1:00 PM PDT
Details: Come prepared with any questions regarding the R training or working in R Studio.



Title: How to read a scientific paper by Anca
When: Thursday, July 9 at 1:00 PM PDT
Details We will be going over what to focus on while reading a scientific paper so that you can understand it as well as possible!



Title: Basic & Advanced Python Programming, Data Interpretation by Priscilla
When: Friday, July 10 at 12:30 PM PDT
Details: None



Title: R, Python, Collaboration by Yoga
When: Thursday, Friday, and Monday, July 9, 10, 13 at 10:00 AM PDT
Details: Come with questions about R, Python, Slack, the Stem Away website, and Google Calendar.



Title: Basic Python and Understanding Figures from the Paper by Alec
When: Tuesdays and Thursdays, July 7th, 9th, 14th and 16th from 6:00 PM PDT
Details: For those asking about figures, you should ideally come with some specific plots in mind.



Title: Data Visualization using R by Priya
When: Wednesday , July 8 at 10:00 AM PDT
Details: Install R & R Studio



Title: Handling data sets in R by Alicia
When: Monday, July 13 at 11:00 AM PDT
Details: Please download and install R and R Studio, as well as the .tar file found at the bottom of the following website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8671. Also, please be familiar with the concepts in the R training videos from 6/02, 6/05, 6/09, and 6/12



Title: Introduction to R for Visualization (ggplot, heatmaps, PCA) by Anya
When: Monday, July 13 at 9:00 AM PDT
Details Please download R and RStudio and be familiar with concepts in the R training video from 6/05 before you come.



Title: Basic Programming in Python (Part 1) by Goral
When: Wednesday, July 15th at 2:00 pm PDT
Details: Please download Jupyter Notebook via Anaconda before you come to this session
1 Like

Where could I find the assessment? Is this assessment for all ?

Only participants and observers. Not leads.

Some of the google meets talk about Python, but I do not see any training materials about it so should we learn it on our own?

Not including Python in the self-assessment step. But it will be used in the final project as an optional step for data visualization beyond what R can do.

I am applying to be a bioinformatics observer and I have no experience in R and the webinars have helped. I am really trying to use Asana but I am stuck, I have watched the videos in the drive and they have helped a little bit. But, do I still have a chance of getting the internship If I am unable to carry out these tasks successfully?

Hi Trisha, The Bioinformatics pathway is one of the more challenging ones. Even in an observer role, you will not get much out of the experience if you are struggling with R. Also, keep in mind that the whole experience of working virtually in new teams will also be challenging.

Is there any other pathway that appeals to you? Maybe try that first? Try Bioinformatics when you have some basic comfort level with programming. Machine Learning or Full Stack also require some basic comfort level with programming.

@ddas Thank you for your response, I do have experience in other programming languages, I don’t think that it is the programming so much, but it is the project structure and organization. For instance, on Asana, I am not sure if I should be in a Bioinformatics team, and how that would work. As an observer, I would just want exposure to the bioinformatics field.

Got it! The questions related to tool usage will be fairly simple. However, note that during the project, you have to use these tools to observe the project. The observer role is not set up to be an academic experience. You will get the exposure but in an industry environment. Learning to use collaboration and project management tools is an integral part of the virtual internships.

Okay, sounds good, I will just familiarize myself with these tools during this time, so that I will be able to use them to observe the project. Thank you!

I am in the same boat as Trisha_N, and hope to gain exposure to the field of bioinformatics. Although I am unfamiliar with python and R (I’ve used codecademy to explore python), I am familiar with NCBI and PubMed and have used these sites to look into research papers to answer my own burning questions. I believe that dry lab skills will be necessary in my future.

When will the self-assessment be assigned or posted in Drive for bioinformatics? (as I believe the self-assessment is due on 07/17)

1 Like

Hi @yvesgaetan! I think there may be a spelling mistake on one of the questions in the second quiz? Referring to the volcano plot, it says “unregulated” genes but I’m guessing this is actually meant to be “upregulated”? This might be important to note/change before others take the quiz as the misunderstanding meant I got the answer incorrect. I hope this helps!:))

Thank you @sona. And congratulations on becoming the first new student to join the July session :slight_smile:
Your scores are great. But it is your self-assessment part that tells me that you will both learn from this experience and be an asset to your team. Welcome!

@yvesgaetan: I have corrected the typo for now, I believe Sona is right. But please double check tomorrow.

The corrected question is:

Looking at the previous plot, which color indicates upregulated genes?

Thank you @ddas !! I’m excited to get started.

Hi @Sail19, I admire your enthusiasm and curiosity about Bioinformatics! A link to the self-assessment is at the top of this page :wink: Self Assessment Form

Hi team. Just finnished the Self Assessment Form and I was wondering if we will have some more details about the data pipeline in R? I’m really excited to work with you and to make an impact together. Also, after self assesment we will be assign to a team or a group?

Hi Maria, we will be hosting a webinar tomorrow to introduce the pipeline. You will continue working on your own with help from office hours this week and start in teams from next week. Very happy to see students so excited to start! Welcome!

1 Like