- Concise overview of things learned:
- Technical Area: I have attended all of the R trainings conducted by Yves and learnt more about the applications of various packages in R to analyse data and metadata and construct better data visualisation tools. I learnt more about using ggplot2, constructing heat maps, volcano plots, etc. Python was a new programming language for me, and I understood more about how it functions as an object-orientated language and the differences in the functions, data types and classes between python and R.
- Tools: New packages in R programming (mainly for data visualisation), Python (basics)
- Soft Skills: Attending talks from Debaleena and Stephanie, made me appreciate the importance of communication and networking in industry. I updated my LinkedIn, and managed to connect with as many people I can in my team. Through happy hours and team meetings, I had the opportunity to build connections with my team members and learn more about their experiences, so we can work together further into this project, with our shared knowledge.
- Three Achievement Highlights:
- Going over the scientific paper and understanding the background knowledge for the paper as I personally do not come from a genetics background.
- Keeping up with all the technical training sessions in R and understanding the new functions used the various packages and their different arguments.
- Connected with other team members on LinkedIn and getting to know my team leaders better
- List of meetings/ training attended including social team events:
- I attended all the Team 1 and now Bioinformagic Team meetings
- All the R training sessions (4 sessions so far)
- I attended the technical training webinars and logistics webinars
- I have attended the beginner Python training session last week
- I have attended the welcome sessions from Stephanie and Debaleena
- I attended the team happy hour for the first week, but was unable to attend the second one due to a family emergency
- Finally, I attended the Office Hours with the team leads, which allowed me to get clarifications on some technical questions
- Goals for the upcoming week:
- I aim to make a to-do task list everyday, so that I can keep up with all the work that will be assigned, and keep track of my progress through this internship. I also aim to regularly communicate with my team members, as we have been placed into smaller teams to complete the weekly deliverables and organising the next happy hours.
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Self-Assessment #2:
- Concise overview of things learned:
- Technical Area: The recent R assignments and the week 3 deliverables have helped me improve my R skills and I have learnt more in dealing with the large microarray data, producing quality control checks on the data (our team used AffyPLM) and finally visualise our results using ggplot2 and also producing principal component analysis (PCA) Tools: More new packages within R (within the Bioconductor package) and R studio
- Soft Skills: Working on our first set of deliverables with our new smaller teams, has helped me a lot in engaging more with my teammates, creating better communication with them and us working together to finish the tasks. I also connected with more people on LinkedIn
- Three Achievement Highlights:
- Working on the week 3 deliverables and getting help from both my teammates and my leads by going to office hours and through the StemAway forum.
- Improving my R skills by looking up certain functions and packages that are new to me on google and other forums on the internet
- I have made many more connections on LinkedIn and managed to find and follow my interests and companies I might be interested in working
- List of meetings/training attended including social team events:
- I have attended the Asana training and the Technical Training webinars last week
- I have attended the Bioinformagic Team meetings that were held last week and also the one held this week
- I attended the Python and pandas webinar
- I have attended to the office hours with the team leads last week to get help with my tasks
- Finally, I attended the happy hour with my team on Friday and we engaged in a fun Family Feud game
- Goals for the upcoming week:
- For this week's deliverables, I aim to do my best to work on the tasks early, so that I will be able to connect with my team leads and get their help either through the office hours tomorrow or through the StemAway forum.
- I also aim to better connect with more of my teammates as we will be working with two other teams to compare our results from last week's tasks and work together to produce a presentation of our analysis
- A detailed statement of tasks done:
- For the week 3 deliverables, my team worked together to complete the tasks and then we were able to compare our work during our regular team meetings and then compile everything together for our final document
- We ran into a couple of errors and problems and I tried troubleshooting them with my teammates first and then we sought out help from our team leads
- I managed to get onto Asana and the slack platform and learn how to better use them
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Self-Assessment #3:
- Concise overview of things learned:
- Technical Area: I have learnt using more packages within R and the Bioconductor software and used these to generate differential gene analysis on our normalised data from last week. We used the limma package and also produced more volcano plots from the output of our analysis
- Tools: More R packages (within Bioconductor), R studio, Python and Jupyter notebook
- Soft Skills: Connected with more of my teammates and other interns from Stem-Away. I also liked and followed more companies that I might be interested in working
- Three Achievement Highlights:
- Learnt more about gene filtering, and then analysing the data with limma package
- Attended office hours and also took help from the leads and mentors by connecting with them on the Stem-Away forum and slack to complete the week's deliverables
- I worked more efficiently with my team members and we connected more frequently, helped each other and managed to work through our tasks
- List of meetings/training attended including social team events:
- I have attended the Bioinformagic Team meetings last week and the one yesterday.
- I attended the R training and the GitHub tutorial
- I also went to the Office Hours and finally the Team Happy Hour
- Goals for the upcoming week:
- Start working on the deliverables early, giving us more time to ask questions and be able to work through them, as our team experienced a lot of problems and working through them earlier would have helped us
- I also aim to network more on LinkedIn to professors whose research I am interested in or employees in companies that interest me
- A detailed statement of tasks done:
- Completed the week 4 deliverables, there was a slight delay in submission due to problems our team experienced, but we worked through them and managed to complete all the tasks
- I joined GitHub and downloaded Git and started working through the Python exercises on Jupyter notebook
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Self-Assessment #4:
- Concise overview of things learned:
- Technical Area: Following through the project, and working on Week 5 deliverables, I have learnt more about many different analyses that can be done on our differentially expressed genes. These include Gene Ontology (GO) Analysis, KEGG Analysis, WikiPathways analysis and finally external tools including EnrichR.
- Tools: R studio, GitHub, Asana, EnrichR
- Soft Skills: I am continuing working with my Team and with other teams to produce the weekly presentations and also improve my communication skills with my teammates, as we work on the tasks together
- Three Achievement Highlights:
- I learnt more about the various analysis that can be done on our gene data and been working through the Week 5 deliverables at a much better pace compared to the previous weeks
- I managed to troubleshoot some of my code from last two weeks which was creating few errors on our Week 4 results by taking help from technical leads during Office Hours
- I applied to be a lead for the July session and I am very excited to be taking on this new role and working with the other leads
- List of meetings/training attended including social team events:
- I attended the Bioinformagic Team meetings last week and the one on Monday this week
- I attended the R office hours and also the second GitHub tutorial
- I also attended the Technical Training with the Mentors yesterday and this gave me a chance to meet the other mentors and leads and also Debaleena
- Goals for the upcoming week:
- Me and my teammates have worked more efficiently this week and are more unto date with our deliverables and I hope that we can work with the other Team and create a good presentation of our work
- I also aim to communicate and get in touch with the mentors more and the new leads through the meetings and technical trainings
- A detailed statement of tasks done:
- Completed the Phenotypic Data Analysis by downloading the matrix data from the GEO database, cleaning the data and creating a new expressionset which contains the phenodata and our original data
- Worked with Team Wand to present our results from Week 4 and also be able to compare our volcano plots
- Working currently on the last part of Week 5 deliverables and aim to get in touch with the other Team to compare our analyses and present it in the next team meeting
- Met with Debaleena and the other mentors and leads for Bioinformatics and hope to build better relationships and connect with them more throughout the meetings
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Self-Assessment #5:
- Concise overview of things learned:
- Technical Area: Completed working through Week 5 deliverables, and learnt more about Gene Ontology (GO) Analysis, KEGG Analysis, WikiPathways analysis and finally external tools including EnrichR. Worked with Team Wand and Team Slytherin to present our results and compare between our teams.
- Tools: R studio, R, GitHub, Asana, EnrichR
- Soft Skills: I have greatly improved on my communication skills since the beginning of the internship, and am able to reach out and talk more effectively to get my points across to my teammates, leads and mentors.
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Three Achievement Highlights:
- While working on the presentations for the Week 5 deliverables, I learnt more about Gene Ontology (GO) Analysis and EnrichR, by watching the Technical Training Webinars hosted by Ali and reading up about them on google.
- I continued to effectively communicate with my teammates and the other Teams within Bioinformagic
- I managed to reach out and connect with the new leads for the July Session and also ask required questions to help me choose the right lead position for me from the current leads
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List of meetings/training attended including social team events:
- I attended the Bioinformagic Team meetings last week and the one on Monday this week
- I attended the office hours and also the team happy hour
- I also attended the Technical Training with the Mentors yesterday and also the meeting with the old leads and the new leads, allowing me to ask questions to find out more the various lead roles
- I attended the Leadership skills meeting with Stephanie
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Goals for the upcoming week:
- I plan to go through the colorectal paper and see how everything that we have learnt so far is put together in terms of bioinformatics and create a final presentation, taking the help of Office Hours and all the other available resources
- I also plan to connect more on LinkedIn, and also update my LinkedIn profile with all my past experiences
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A detailed statement of tasks done:
- Completed the Week 5 deliverables, and better understood about various tools to conduct functional analysis on our gene data, including GO Analysis, KEGG Analysis, WikiPathways analysis and EnrichR
- Worked with Team Wand and Team Slytherin to present our results from Week 5 and also learn more about GO Analysis and EnrichR
- Met with the other mentors and leads for Bioinformatics and connected with them through the meetings and technical training webinars
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Self-Assessment #6:
- Concise overview of things learned:
- Technical Area: Worked through the Week 7 and 8 Deliverables, applying everything that we have learnt so far from QC control to normalisation and analysis on a new genomic data set, GSE21510
- Tools: R studio, R, GitHub
- Soft Skills: I have worked a lot on my presentation skills and lead the the new team meeting for the July Bioinformatics session and also a webinar explaining through the biological definitions and scientific terms that are in the paper
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Three Achievement Highlights:
- I went over the paper again completely, to understand their pipeline and the steps they followed to analyse the data, and compared it to our analysis
- I worked through the steps that we have learnt so far and applied it to a new dataset
- I worked through the deliverables, while also leading my new team for the July session and getting my teammates onboarded into the internship
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List of meetings/training attended including social team events:
- I attended the Bioinformagic Team meetings
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Goals for the upcoming week:
- I hope to give a good final presentation, showcasing all my work done, applying everything that we have learnt so far to a new dataset and analysing the paper we studied and putting everything together to a get a more detailed understanding of how our analysis fits in with the papers
- I have updated most of my LinkedIn profile and will continue to connect with more professors and employees of companies that I am interested in
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A detailed statement of tasks done:
- Worked through Week 7/8 Deliverables to better understand the pipeline of the paper, working through QC control, normalisation and analysis to produce differentially expressed genes and then visualise my results in a volcano plot and a heatmap
- Met with the new July team participants and observers and worked with the other team leads to out together a team meeting and a technical training webinar
Final Self-Assessment (#7):
- Concise overview of things learned:
- Technical Area: How to analyse large scale genomic data, using R and also the GEO database, starting from: downloading and reading the dataset, cleaning the data and assessing the quality control of data, normalising the data, to make it more easier to read and analyse, annotating the genes, filtering the dataset, Limma analysis, and finally visualisation using heatmaps, volcano plots and also PCA plots. I also understood what my analysis and results show by performing functional analysis using Gene Ontology, KEGG and WikiPathways. I also learnt how to interpret my analysis and applying it back to the paper and understanding how it fits in with the main purpose of the paper.
- Tools: R studio, R, GitHub, Also gained more understanding of python language and Jupyter notebook
- Soft Skills: Working and interacting with my team and sub-teams on a virtual platform. Connecting with my teammates and networking on LinkedIn, building a better professional network. Putting together presentations every week with my teammates, to showcase our results, findings and also reflect on our work to see the challenges we faced, how we can overcome them, and also what we can do better for the next time. I have gained more communication, time-management and also project-management skills.
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Three Achievement Highlights:
- I worked through each step of the analysis and everything that we have learnt, applying it to the final dataset
- I have better knowledge of R, using the Bioconductor packages in R and using R overall
- I have gained a better understanding and appreciation for the filed of bioinformatics, and can now build a connection between biology and data science and use data science tools to better understand biology
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Goals for the upcoming week:
- Learning the whole pipeline and the analysis that is going into understanding these large scale genomic datasets and the results and interpretations that you can get from them has really fascinated me and I am excited to carry on and apply everything that I have learnt onto my further research in my area of study in neuroscience
Thank you so much @egunduz, @yvesgaetan and @Isha for a wonderful internship experience. I look forward to using all the new technical skills I have learnt into my lab classes and research project in the coming year!
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Here is an attachment of my final presentation:
Ashlesha_Patil_Final Presentation_ Week 7&8 Deliverables.pdf (990.6 KB)
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It was so wonderful meeting you Ashlesha, wishing you all the best in your future endeavors! Stay in touch 