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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to conduct basic differential gene expression analysis through R. I have learned functions to normalize data, do principle component analysis, and form volcano plots to show fold changes in genes across various patient conditions.
Tools: I have learned basic python programming skills. I have also become more comfortable with data visualization through packages such as numpy and pandas. In R, I have become more accustomed to the ggplot2 package and its uses in data visualization.
Soft Skills: I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. I appreciate the level of communication provided by the team-leads to help me develop my skills in time-management and project-management. -
Three achievement highlights
During team-building exercises, I have more become open with my peers and can convey my appreciation of bioinformatics with like-minded individuals. In terms of programming, I have kept up-to-date with the packages and functions available to me when conducting data analysis. Overall, I am starting to understand the connection between programming and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars (1,2,3), watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. I was not able to make it to the happy hour social event, but look forward to it in the future! -
Goals for the upcoming week.
My goals include to get comfortable with the first part of the project which is data quality control. I aim to understand the programming and conceptual importance of each step in this pipeline-planned project. Another goal is to develop my proficiency in programming in R where using the functions become second-nature. My last goal is to get to know my team members more.
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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to conduct basic differential gene expression analysis through R. I have learned functions to create volcano plots and to use a gene annotation library to determine locations of genes within tissue samples. I have become more comfortable with the Limma package and have learned how to create a design matrix which is used in part of the linear fit modelling. This fit is then used to find the top # of genes using the topTable() function.
Tools: I have learned basic R programming skills. I have also become more comfortable with data visualization through packages such as ggplot2 and Limma In R. I have become more accustomed to the ggplot2 package and its uses in data visualization. I have learned how to use Asana and GitHub and am starting to appreciate its uses in the work-field.
Soft Skills: I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. I appreciate the level of communication provided by the team-leads to help me develop my skills in time-management and project-management. I have reached out to leads when I have difficulty in assignments and we have developed a friendly relationship through this. -
Three achievement highlights
During team-building exercises, I have more become open with my peers and can convey my appreciation of bioinformatics with like-minded individuals. In terms of programming, I have kept up-to-date with the deliverables to ensure proper understanding of the skills being taught. Overall, I am starting to understand the connection between programming and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars, watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. I was not able to make it to the happy hour social event, but look forward to it in the future! -
Goals for the upcoming week.
My goals include to get comfortable with the week 5 deliverables of the project which is utilizing the pathway information like KEGG. I aim to understand the programming and conceptual importance of each step in this pipeline-planned project. Another goal is to develop my proficiency in programming in R where using the functions become second-nature. My last goal is to get to know my team members more and utilize technological resources in a more efficient manner.
1 Like
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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to conduct gene ontology analysis. I learned how pathway and network tools, like GO and KEGG analysis, can be used to show which classes of genes are over-represented in cancer vs control states. I have become more comfortable in knowing how to use external tools like Metascape to generate barplots, dotplots and network maps of genes. Overall, I have become more acclimated in comparing results from multiple data analysis packages.
Tools: I have performed gene ontology and gene set enrichment analysis through the clusterProfiler package. I have also become more comfortable with data visualization through packages such as ggplot2 and Bioconductor In R. I have learned how to use Asana and GitHub and am starting to appreciate its uses in the work-field.
Soft Skills: I have learned how to present deliverables with a team in a more effective manner. I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. I appreciate the level of communication provided by the team-leads to help me develop my skills in time-management and project-management. I have reached out to leads when I have difficulty in assignments and we have developed a friendly relationship through this. -
Three achievement highlights
During team-building exercises, I have more become open with my peers and can convey my appreciation of bioinformatics with like-minded individuals. In terms of programming, I have kept up-to-date with the deliverables to ensure proper understanding of the skills being taught. Overall, I am starting to understand the connection between programming and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars, watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. I was not able to make it to the happy hour social event, but look forward to it in the future! -
Goals for the upcoming week.
My goals include to prepare the presentation of the week 5’s deliverables. I also want to gain a deeper understanding of the pathway and gene ontology analysis from a biological standpoint. I aim to understand the programming and conceptual importance of each step in this pipeline-planned project. Another goal is to develop my proficiency in programming in R where using the functions become second-nature. My last goal is to become more proactive and utilize technological resources in a more efficient manner.
1 Like
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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to conduct gene ontology analysis. I learned how pathway and network tools, like GO and KEGG analysis, can be used to show which classes of genes are over-represented in cancer vs control states. I have become more comfortable in knowing how to use external tools like Metascape to generate barplots, dotplots and network maps of genes. Overall, I have become more acclimated in comparing results from multiple data analysis packages. I have learned how to use KEGG analysis and WikiPathway analysis tools.
Tools: I have performed gene ontology and gene set enrichment analysis through the clusterProfiler package. I have also become more comfortable with data visualization through packages such as ggplot2 and Bioconductor In R. I have learned how to use Asana and GitHub and am starting to appreciate its uses in the work-field.
Soft Skills: I have learned how to present deliverables with a team in a more effective manner. I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. I appreciate the level of communication provided by the team-leads to help me develop my skills in time-management and project-management. I have reached out to leads when I have difficulty in assignments and we have developed a friendly relationship through this. I have also tried different resources to accommodate the needs of various teammates. -
Three achievement highlights
During team-building exercises, I have more become open with my peers and can convey my appreciation of bioinformatics with like-minded individuals. In terms of programming, I have kept up-to-date with the deliverables to ensure proper understanding of the skills being taught. Overall, I am starting to understand the connection between programming and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars, watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. I was not able to make it to the happy hour social event, but look forward to it in the future! -
Goals for the upcoming week.
My goals include to start the final project deliverables for week 7/8. I also want to gain a deeper understanding of the pathway and gene ontology analysis from a biological standpoint. I aim to understand the programming and conceptual importance of each step in this pipeline-planned project. Another goal is to develop my proficiency in programming in R where using the functions become second-nature. Another goal is to understand the pipeline and be able to reproduce and use it in a different scenario. My last goal is to become more proactive and utilize technological resources in a more efficient manner.
1 Like
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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to conduct gene ontology analysis. I learned how pathway and network tools, like GO and KEGG analysis, can be used to show which classes of genes are over-represented in cancer vs control states. I have become more comfortable in knowing how to use external tools like Metascape and String to generate barplots, dotplots and network maps of genes. Overall, I have become more acclimated in comparing results from multiple data analysis packages.
Tools: I have performed gene ontology and gene set enrichment analysis through the clusterProfiler package. I have also become more comfortable with data visualization through packages such as ggplot2 and Bioconductor In R. I have learned how to use Asana and GitHub and am starting to appreciate its uses in the work-field. I have become more comfortable with external data tools.
Soft Skills: I have learned how to formulate a presentation by myself in a more effective manner. I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. I appreciate the level of communication provided by the team-leads to help me develop my skills in time-management and project-management. I have reached out to leads when I have difficulty in assignments and we have developed a friendly relationship through this. -
Three achievement highlights
During team-building exercises, I have more become open with my peers and can convey my appreciation of bioinformatics with like-minded individuals. In terms of programming, I have kept up-to-date with the deliverables to ensure proper understanding of the skills being taught. Overall, I am starting to understand the connection between programming and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars, watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. I was not able to make it to the happy hour social event, but look forward to it in the future! -
Goals for the upcoming week.
My goals include to prepare the presentation of the week 8’s deliverables. I also want to gain a deeper understanding of the pathway and gene ontology analysis from a biological standpoint. I aim to understand the programming and conceptual importance of each step in this pipeline-planned project. Another goal is to develop my proficiency in programming in R where using the functions become second-nature. My last goal is to become more proactive and utilize technological resources in a more efficient manner.
Final Self Assessment
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Concise overview of things learned
Technical Area: In the past few weeks, I learned how to create and optimize a bioinformatics project pipeline. I have learned how to conduct microarray data set quality control and normalization techniques. I have learned how to conduct gene annotation analysis and gene filtering. Then, I was able to understand the analysis of differentially expressed genes using the Limma package. With this, I was able to perform Gene Ontology, Wikipathway, KEGG pathway, and Protein-Protein Interaction analysis. Overall, I learned from a biological standpoint on how to detect prognostic markers for colorectal cancer and how to visualize which classes of genes are differentially expressed in cancer vs control states using ggplot2. I have become more comfortable in knowing how to use external tools like Metascape and String to generate barplots, dotplots and network maps of genes. Overall, I have become more acclimated in comparing results from multiple data analysis packages and analyzing/interpreting the results.
Tools: I have performed data quality control, gene annotation, analysis of differentially expressed genes, gene ontology and gene set enrichment analysis, through the Bioconductor package. I have become more comfortable with external data tools such as STRING and Metascape. I have also become more comfortable with data visualization through packages such as ggplot2 in R. I have learned how to use Asana and GitHub and am starting to appreciate its uses in the work-fields.
Soft Skills: I have learned how to formulate a presentation by myself in a more effective manner by brainstorming the general structure and the necessary details required. I learned the techniques to deliver a professional presentation to mentors and scientists currently in the field of bioinformatics. I have learned how to interact with team-members and leaders more productively and how to ask questions and convey interests in a friendly environment. The internship has helped me develop my skills in time-management and project-management. It has taught me how to reach out to local alumni and steps to take to build one’s professional network. -
Three achievement highlights
During the final deliverables of the internship, I designed my own project pipeline utilizing a different dataset to study prognostic markers for colorectal cancer. I completed all weekly deliverables for the entire internship in a timely manner and presented results to peers. Through this internship, I have understood the Biocondutor package at a more complex level and have started to gain an appreciation of its uses within the bioinformatics industry. Overall, I am starting to understand the connection between programming, data science, math (statistics), and biology within bioinformatics. -
List of meetings/ training attended including social team events
I have been to all the meetings including the technical training webinars, watched all the R-training videos, and attended some Python training videos and watched the rest of them through the recorded lectures. -
Goals for the upcoming week.
My goals include to utilize the technical skills learned to develop a new project pipeline that includes “survival analysis”. Another goal is to expand the data science techniques learned in R and apply them in a workplace setting. My other goal is to use the technical skills learned for non-microarray data. My overall goal is to gain a deeper understanding for the field of bioinformatics.
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Here is the attached presentation: Siddiqui. Week 8 Deliverables.pdf (1.6 MB)
Thank you @egunduz, @yvesgaetan, and @Isha for all your help and for providing an insightful experience!
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Great meeting you Zayyad, all the best!