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Mentorship

-Last updated: Nov 2023 +Last updated: Dec 2023
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Research Mentorship

-Last updated: Nov 2023 +Last updated: Dec 2023
diff --git a/docs/listings.json b/docs/listings.json index 7e29798..6df9350 100644 --- a/docs/listings.json +++ b/docs/listings.json @@ -4,6 +4,7 @@ "items": [ "/posts/2023-11-29-notion-research-dashboard/index.html", "/posts/2022-12-04-GAAP/index.html", + "/posts/2024-02-03-xetthecum-storymapping/index.html", "/posts/2021-10-24-writing-strategies-for-government-scholarships/index.html", "/posts/2022-01-30-galiwatch/index.html", "/posts/2021-11-08-undergraduate-research-at-uoft/index.html", diff --git a/docs/search.json b/docs/search.json index 1d5cae1..8a93249 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1,150 +1,108 @@ [ { - "objectID": "posts/2023-11-29-notion-research-dashboard/index.html", - "href": "posts/2023-11-29-notion-research-dashboard/index.html", - "title": "Research dashboard in Notion", + "objectID": "posts/2024-02-03-xetthecum-storymapping/index.html", + "href": "posts/2024-02-03-xetthecum-storymapping/index.html", + "title": "Xetthecum", "section": "", - "text": "I use notion to organize lots of things, in particular my research notes. I used to use R Markdown, which was great for mixing text, images, \\(\\LaTeX\\), code, and (most importantly) emojis. However, over time my research notebook got bloated and trying to keep notes and also make sure everything rendered correctly became challenging.\nI moved to Notion because it offers a very similar experience for markdown lovers.\nPeep my template here!" - }, - { - "objectID": "posts/2023-11-29-notion-research-dashboard/index.html#thoughts-on-the-experience", - "href": "posts/2023-11-29-notion-research-dashboard/index.html#thoughts-on-the-experience", - "title": "Research dashboard in Notion", - "section": "Thoughts on the experience", - "text": "Thoughts on the experience\nHere’s some things I like about it:\n\nCloud backed + mobile app\nAll my notes are searchable\nPossible to export as markdown\nDatabases! Every page can be a database and it’s pretty cool\nTemplates! I use the “new experiment” button to add structured entries to my lab notebook\nEvery page can be reformatted and nested on the fly\nI can sync TODOs across multiple pages: my main planner, and each project’s respective TODO list\nUseful shortcuts for Today’s date and cross referencing other pages\nThere are some cute templates out there\n\nAnd some gripes:\n\nNo offline mode - even for simple notes!\nSearch UI is not great: can’t search within code chunks, or toggle sections\nMarkdown exports are clunky and not everything will be well preserved (especially images)\nAdmiring cute templates feels productive, but it’s actually a massive time sink" + "text": "I am working with designer at the Inclusive Design Research Center at OCAD to build a nice website for the IMERSS ecocultural mapping project.\nProject info IMERSS\nRetreat Cove (Xetthecum in the Hul’qumi’num language) has a special place in my heart and growing up I spent lots of summers in the area.\nParticipating in this project means that I got to read loads of interesting information put together by the team, and I learned a" }, { - "objectID": "posts/2022-01-30-galiwatch/index.html", - "href": "posts/2022-01-30-galiwatch/index.html", - "title": "Operation Galiwatch", + "objectID": "posts/2022-12-04-GAAP/index.html", + "href": "posts/2022-12-04-GAAP/index.html", + "title": "Reflection on Toronto GAAP", "section": "", - "text": "My parents got into birdwatching… at scale. They’ve set out to thoroughly document what’s going on in their yard on Galiano Island, BC: Operation Galiwatch.\nWe’ve set up a bunch of sensors to collect air quality data, weather information, and timelapse images. We’re monitoring all sorts of pollinators, such as bees and humming birds. If all goes well with the infrared camera, maybe even bats.\nI’ve been helping debug the setup, doing data analysis, and maintaining the Galiwatch website.\nWe’re collaborating with the folks at Biodiversity Galiano and IMERSS to make low-cost, hyperlocal ecosystem and climate monitoring accessible for other citizen scientists!" + "text": "It’s my second time organizing the Toronto CS Graduate Application Assistance Program and it was a great experience!\nThe program matches current Computer Science graduate students with prospective students, with a focus for those who are underrepresented in computing. We were able to provide application feedback to 55 mentees.\nBig thanks to the volunteers for their work 🌻 we got lots of positive coments and grateful messages from mentees.\nI’m looking forward to running this program again next year!" }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html", - "title": "Writing strategies for Canadian scholarships", + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html", + "title": "Undergraduate research at UofT", "section": "", - "text": "This post is my attempt to compile what I’ve learned about writing though applying for government scholarships. Most of it comes from my own trial and error, but some I also picked up from workshops1, and by looking at other people’s proposals 2.\nDisclaimer: I’m not a writer by training, and I definitely haven’t won all the awards I’ve ever applied to. This is really just a list of things that I wish I knew the first time I applied to government scholarships. All the following tips are aimed at building technical project proposals, with a bias towards NSERC because that’s the agency that my work falls under." + "text": "This post is aimed primarily at students interested in computational biology and machine learning, but not restricted to these areas by any means." }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#general-advice", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#general-advice", - "title": "Writing strategies for Canadian scholarships", - "section": "General advice", - "text": "General advice\n\nUse a citation manager\nIf you’re not already using a citation management tool, then your life is harder than it needs to be. I use Zotero, but some people prefer Mendeley, or Paperpile, for example.\n\n\nI explain all the reasons I love Zotero here.\n\n\nDon’t expect to nail it on the first try.\nA common theme seems to be “I didn’t get any awards at all at first, then something clicked and I seemed to get them all at once”. You will probably have to apply several years in a row before you have a good grasp on the language to use to describe your problem, and build a strong understand where your work fits within the field as a whole.\nLuckily, the easiest thing to work off of is your own past writing. If you start early, you will become a valuable resource to your future self 😁\n\n\nGet writing help\nMany universities have a writing center, with workshops aimed at specific scholarships. Look into their calendar ahead of time, as you’ll get the most out of it if you can bring a draft with you.\n\n\nGet someone else to read it\nBonus points if they are not in your field, and are able to grasp your research proposal enough to get excited about your problem. This is a good litmus test for writing clarity." + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#resources", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#resources", + "title": "Undergraduate research at UofT", + "section": "Resources", + "text": "Resources\nBefore I say anything at all, I must promote the excellent advice that others have compiled.\nThis is a small selection of my personal favourites, but many of them link out to even more resources.\n\nReview of Undergraduate Computer Science (RUCS) and their fabulous Undergraduate Research Guide\nThe Bioinformatics and Computational Biology Student Union (BCBSU) hosts and annual information session on research courses BCB330 & BCB430\nTips on finding a supervisor from the BCB program" }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#an-algorithm-to-write-to", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#an-algorithm-to-write-to", - "title": "Writing strategies for Canadian scholarships", - "section": "An algorithm to write to", - "text": "An algorithm to write to\nI use this same process for both technical writing, and personal statements. This is what works for me personally: take what you like and ignore the rest 😊\n\n\n\n\n\n\nWarning\n\n\n\nI am writing this in 2022. The specific formatting instructions might have changed since then. Never listen to anyone about presentation standards, except the official instructions.\n\n\nDo the following things in this order:\n\nSet up page margins to 2cm\nSet font to 12pt Arial\nWrite the title and your name in the header. Don’t forget to paginate where appropriate.\nPaste the instructions into the document, anything that gives guidelines on what the content should be. Check back on these as you write, especially if you get stuck on what to write about.\nWrite a bullet point outline of all the ideas you want to include (past/present/future work, practical implementation, etc)\nWrite statement-style headers for each section, in a way that captures the narrative flow of the story. These headers should be written such that they are sufficient that someone reading them could explain your whole project, even though you haven’t written the content yet. Put them in bold.\nAssign the bullet points to headers. These will guide how you flush out the body text.\nWrite the content paragraphs. Don’t worry about writing them in order. If you have trouble making progress on one, write a brief skeleton the best you can, and move on to a different section. The headers from step 5 will give you a strong sense of which chunks of text are self-contained.\nEdit. Go back to any paragraphs that are not flowing correctly. Use a read-aloud service (ex. in Word) to listen to your draft.\nRealize you’re about 20% over the page limit. Change font to 12pt Times New Roman. Now you’re done.\n\n\n\nSteps 5 & 6 should only contain sentence fragments and ideas that are easy to write. Do not spend time agonizing over wording in these steps.\n\n\n\n\n\nI learned #6 by reading other people’s examples. Done correctly, your headers will greatly improve readability. Ultimately you want your writing to be as skimmable as possible. This is important, because your application will be one of a large number of others that reviewers will have to read through.\n#10 is also a critical trick for me: always draft in Arial before finalizing to Times New Roman. TNR is much more condensed, and this font conversion will gift you extra space, as long as you don’t start by writing in it. I tend to over-write, and this trick helps me avoid having to spend a lot of time cutting content.\nWhen it comes to getting the exact wording you want, don’t let perfect be the enemy of progress. When you get stuck on a word:\n\nUse a thesaurus\nLook at other writing samples (some of mine are available here)\nWrite down a few synonyms of the word you’re trying to find as a note to self and come back to it later." + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#research-comes-in-many-shapes-and-sizes", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#research-comes-in-many-shapes-and-sizes", + "title": "Undergraduate research at UofT", + "section": "Research comes in many shapes and sizes", + "text": "Research comes in many shapes and sizes\nUniversity of Toronto is part of a rich research ecosystem in Toronto, and if you want to try out research as an undergrad, this is a great place to do it! In addition the University labs, many professors from associated institutes are able to take on UofT students for research. To name a few:\n\nUnited Health Netowrk\nSickKids Hospital\nLunenfeld-Tanenbaum Research Institute\nOntario Insitute for Cancer Research\nData Sciences Insitute\nVector Institute\n\nAs an undergrad, I was in the Bioinformatics and Computational Biology program 2015-2019. As part of the requirements for that program, I took two research project courses; BCB330 and BCB430. There are many similar courses offered through a variety of programs, such as ROPs, capstone projects, independent research projects, etc. Most of these are blank-cheque style courses you get credit for by working with a professor in a research capacity.\nSometimes you can get a paid research position supported by a USRA grant. These are grants offered by the Canadian government to encourage labs to hire undergraduate students for summer research positions.\n\n\n\n\n\n\nNote\n\n\n\nDon’t apply on your own! The USRA proposal expectations are particular, and field-specific. Ask your professor or research mentor for help with crafting the application.\n\n\n\nCourse-based programs\nOften, you don’t strictly have to be enrolled in a program to take their research course. You can inquire into research offerings in programs such as CSC, STA, BCB, MGY, BCH, CSB, MBP, and more.\n\n\nSummer programs\nA few examples listed here, by no means exhaustive.\n\nDonnelly Center summer studentships\nVector internships\nTCAIREM summer studentships\nDSI Summer Undergraduate Data Science (SUDS) Opportunities Program" }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#ogs-cgspgs-specific-advice", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#ogs-cgspgs-specific-advice", - "title": "Writing strategies for Canadian scholarships", - "section": "OGS & CGS/PGS specific advice", - "text": "OGS & CGS/PGS specific advice\nI have used more or less the same structure for my successful award applications3:\n\nOGS 2021\nPGS-D 2021\nQEII-GSST 2022\nDSI fellowship 2022\n\n\nStructure of the research proposal\n\n\n\n\n\n\nNote\n\n\n\nThis is just one structuring example which I have followed. Don’t feel bound to what I describe here, if your writing heart leads you elsewhere\n\n\nThere are a few points in this structure that are subtly distinct. You should not just paraphrase the same sentence twice for these, which is a pitfall I’ve run into. I have highlighted pairs of elements in this structure should not get conflated, because these elements have different roles in the proposal. Distinguish them from each other by changing the scope of what you describe.\n\nBackground and motivation\n\nWhere we are now (state of the field)\nWhat’s needed (key steps in new knowledge generation)\n\nObjectives and hypothesis\n\nWhat you’re developing (one-liner)\nWhat it will enable (big picture impact of your results)\n\nKnowledge gap (The direction your results will take the field in. Keep it large enough scale/scope that your project does not completely fill this gap, but maybe your project, plus 3-5 years more research would.)\nSignificance (Implications of what your project will enable)\nExperimental and theoretical approach\n\nSummary of 2-3 goals. Goals should describe the overarching themes of what your results will show.\n2-3 aims, with substeps that build to each aim. Aims should be actionable steps you will take, and build on each other logically, however later aims should not strictly rely on the success of earlier aims in order to be possible to execute. (What would you do if the early stuff didn’t work out? You don’t want to leave your proposal vulnerable to that question.)\n\nWhy you are uniquely positioned to execute the research here and now\n\n\n\nPitfalls\nThe biggest challenge for new grad students is not yet having a strong grasp on the state of their field, and how their project fits in that context.\n\nProbably your PI has a good idea of this, and your lab may have an overarching research story that you can tap into. Ask you PI for writing advice!\nThe only other thing you can do to improve on this is to read widely and engage with other researchers in your field. This is more of a student-lifestyle thing than it is writing advice, but it makes for a good researcher (and subsequently, research proposal).\n\n\n\nResearch contributions\nYour research contributions should include everything you did. This also means things that you had shared responsibility with others. (ex. put down writing if you wrote part of the original draft, even if someone else also wrote part). I recommend referring to CRediT taxonomy for a list and description of roles.\n\n\nRelevant Activities\nI treated this section as place to highlight my non-research CV items. They should ideally have some tie-in to your career goals, and speak to your attributes as a researcher. See Create a draft that harmonizes with your reference letters below." + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#dont-work-for-free", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#dont-work-for-free", + "title": "Undergraduate research at UofT", + "section": "Don’t work for free!", + "text": "Don’t work for free!\nI’ll say it again: don’t work for free!\nYou should either get course credit, or a paycheck for your time. (If you can swing it, get both!) Don’t underestimate the value of your contributions as an undergraduate researcher.\nI hate to see students being taken advantage of via “laboratory volunteer” positions. For one thing, unpaid internships are not legal in Canada.\nIt’s also a big red flag that your work is not being valued as it should be. Chances are that there is a more suitable position out there for you that will serve you better, and compensate you fairly. “Potentially” getting authorship on a publication is not payment." }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#reference-letters", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#reference-letters", - "title": "Writing strategies for Canadian scholarships", - "section": "Reference letters", - "text": "Reference letters\n\nOffer to draft your referee’s letters for them\nThis will make it a lot easier for your referees to agree to be a reference for you. It will also let you have a hand in what your letters look like, and ensure that they highlight the same strengths you show in the rest of the application.\nAt the very least, you should provide your references a few bullet points to work with.\n\n\nCreate a draft that harmonizes with your reference letters\nA common recipe that I have noticed in the successful applications that I’ve seen (and tried to model in my own application) to prove that your leadership is “above and beyond” goes along these lines:\n\nYou have a series of examples of times you were in a leadership position, and did something extra\n\nYou made the leadership position your own in some way\nYou took an active role in supporting others\nYou created something new to solve a problem\n\nBetween your two reference letters, all the examples you listed are repeated, but discussed from a different perspective\nYour referees identify the impact of the “something extra” that you did\nYour referees are able to explain why what you did made others admire/respect/be grateful to you\nYour referees have a lot of positive adjectives to describe your character" + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#choose-a-lab", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#choose-a-lab", + "title": "Undergraduate research at UofT", + "section": "Choose a lab", + "text": "Choose a lab\nMost departments have a list of faculty, this is a good place to start. Survey the landscape of professors that you might work with by looking at their google scholar profile. An easy way to find other similar labs is to click through their co-authors.\nFor an interdisciplinary field such as computational biology, I found it useful to look through the faculty pages of multiple departments, various hospital labs, and start-ups that I knew my peers had done research or PEY at.\n\nCold contacting\nThere are many resources out there for how to compose the dreaded “cold email”, some that I’ve linked to above. Briefly, here is the anatomy of the cold emails I have sent:\n\nintroduce yourself\nexplain what kind of position your looking for\nmention one thing in their recent publication record or lab website that made their research stick out to you\ndescribe any relevant past experience you have\nask for an interview\nattach a cover letter (optional, the email itself may serve as this)\nattach your CV\nattach your transcripts\n\n\n\n\n\n\n\nTip\n\n\n\nAttach your transcripts even if you’re not happy with your grades (I certainly felt this way!) This will increase the likelihood that you hear back and make things go faster. The grades themselves are often not particularly important, but attaching the transcript is a simple way to indicate that you understand what this type of email should contain.\n\n\n\n\n\n\n\n\nTip\n\n\n\nProfessors are generally very busy and terrible at responding to emails. Send a few out to different people, and if you don’t hear back from anyone after about a week, follow up or move on. Radio silence is common, so don’t be discouraged by it." }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#leave-a-full-day-for-formatting", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#leave-a-full-day-for-formatting", - "title": "Writing strategies for Canadian scholarships", - "section": "Leave a full day for formatting", - "text": "Leave a full day for formatting\nDo not underestimate the time sink that is uploading all your files, reuploading, editing the CCV because of a missing comma, reuploading, now there’s an extra comma, reuploading, etc.\nThe first time you put everything into the CCV system is the most painful.\nAfter that it is easier :)" + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#what-to-expect-in-the-research-environment", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#what-to-expect-in-the-research-environment", + "title": "Undergraduate research at UofT", + "section": "What to expect in the research environment", + "text": "What to expect in the research environment\nI divide labs into two categories: Hands-on PI / Hands-off PI\nA Hands-on PI is a professor who has a lot of time for you, but may have high expectations on your research output. Although you may be working with a grad student, this PI could be directly involved in your project and giving you guidance. This environment might be stressful, but you’ll probably learn a lot. Watch out for unreasonable demands.\nHands-off PI has seen it all. Their group is large, and they might not make time to meet with you. They are less obviously invested in your success, but there may be less pressure on you because of this. A grad student is your direct supervisor, and you may work closely with them on their research. In this environment you will have more autonomy, but you will have to be proactive in order to learn. Watch out for feeling isolated or forgotten.\nObviously the Hands-on PI / Hands-off PI labels are not all-encompassing, and most people will fall somewhere in between the two caricatures. Every environment will have its own peculiarities, advantages, and challenges.\nIn all cases you will most likely have a chance to interact with grad students or technical staff. You will get to attend group meetings (usually weekly), and possibly be expected to present your work to the lab at group meeting." }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#vanier", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#vanier", - "title": "Writing strategies for Canadian scholarships", - "section": "Vanier", - "text": "Vanier\nVanier is a different beast. There is a heavy emphasis on leadership, and the expectations are not the same as CGS. Preparing a Vanier application is more work than CGS, and takes more time.\nSilvia Sellán has generously shared advice and examples from her application - which I recommend reading." + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#how-are-research-courses-graded", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#how-are-research-courses-graded", + "title": "Undergraduate research at UofT", + "section": "How are research courses graded?", + "text": "How are research courses graded?\nIn general the grading for research project courses is relatively lax. Often there is a performance evaluation that your supervisor has to fill out at the end, plus some written or presentation-based deliverable for you to submit.\nMany labs will grade you based on your improvement, and you’ll get a good grade as long as you show up regularly and put effort in to learning." }, { - "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#footnotes", - "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#footnotes", - "title": "Writing strategies for Canadian scholarships", - "section": "Footnotes", - "text": "Footnotes\n\n\nShout-out to Daniel Newman↩︎\nSpecial thanks to SG, SS, AD, TS, JW, and SK for helpful advice they’ve shared with me.↩︎\nOf course, I’ve also used it on applications which were ultimately unsuccessful: CGS-M 2019, CGS-D 2020, Vanier 2020, Vanier 2021. However, I’d like to believe that I improved my writing skill over time, and this resulted in my later success.↩︎" + "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#your-research-output", + "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#your-research-output", + "title": "Undergraduate research at UofT", + "section": "Your research output", + "text": "Your research output\nThere are several undergraduate poster days run by various departments, often associated with their respective project courses.\nMost of the summer programs I mentioned above have their own dedicated “research day” at the end of the summer.\nIf this kind of poster day isn’t available to you, one thing you can do at the end of a research experience is to submit to an undergraduate journal or conference. Leave a couple weeks at the end of your research experience for developing a write-up or poster, and ask your mentor for input. With an end product that you deliver in someway to an audience, you will gain more out of your experience, and make it easier to put on your CV.\nSome examples of research-focused UofT student publications:\n\nArbor Journal of Undergraduate Research (The ASSU also hosts an annual undergraduate research conference)\nJULS Journal of Undergraduate Life\nRUCS Review of Undregraduate Computer Science\n\nYou can also apply to have your research appear in similar venues at other universities, or if you’re particularly ambitious, grab some friends and host your own research day 🌈" }, { - "objectID": "posts/2021-05-04-how-to-be-a-good-grad-student/index.html", - "href": "posts/2021-05-04-how-to-be-a-good-grad-student/index.html", - "title": "How to be a good grad student", + "objectID": "posts/2021-09-05-ode-to-zotero/index.html", + "href": "posts/2021-09-05-ode-to-zotero/index.html", + "title": "Ode to Zotero", "section": "", - "text": "Over the last year, I asked several of my mentors this question:\n\nWhat makes for a truly excellent grad student?\n\nI highly recommend you put this question to the people in your life that you work with, and admire. So far, I’ve received several thoughtful answers, but the question often seems to takes people by surprise. This seems funny to me and it made me realize that although a lot of grad students seem to be concerned with “am I doing a good job?” they aren’t asking for help on how to do a good job.\n\n\nObviously you can substitute “grad student” with whatever your current position is. I think this is a valuable question in general for getting perspective on what skills and behaviours you should be investing your time into.\nHere are some of my favourite responses:\n\nThey read a lot. They survey the field and have a good understanding of what’s out there and how their work fits within the context of the research landscape, and how their work is driving the field forward.\nThey are someone who focuses on what the big-picture impact of their project is, and thinks about the ultimate results and their significance.\nThey are a good communicator. They can write clearly, and they can explain their ideas.\nThey know how to make use of their advisor. Often, there are things that an advisor knows a simple answer to, that students don’t find out about just because they didn’t ask." + "text": "Zotero is my citation manager. I love it, here’s why.\n\nIt’s open source\nIt’s lightweight\nIt syncs with overleaf\nIt has excellent search\nOne click to save from browser\nIt syncs to the cloud\nCustomizable bibliography formats\n\nMore reasons to love:\n\nLots of free storage\nIntegreations with Word, Google docs, etc\nThe project folders are great for organizing research\nAutomatic report generation with all your notes\nGroup-libraries for collaboration\nA cute timeline generator\n\n\n\n\nYou can see I got excited about genomics around 2017." }, { - "objectID": "cv_2pg.html", - "href": "cv_2pg.html", - "title": "Cait Harrigan, MSc.", + "objectID": "index.html", + "href": "index.html", + "title": "Hi, I’m Cait", "section": "", - "text": "Cait Harrigan, MSc.\n\ncait.harrigan@mail.utoronto.ca | View this CV online at caitharrigan.ca/cv\nI am a graduate student at the University of Toronto supervised by Quaid Morris and Kieran Campbell. I’m a graduate researcher at the Vector Institute and Doctoral Fellow at the UofT Data Sciences Institute. I use machine learning to understand cancer genomics by modelling the evolutionary constraints that underlie how mutations occur in DNA. I’m passionate about open science, and promoting great mentorship in the sciences." - }, - { - "objectID": "cv_2pg.html#education", - "href": "cv_2pg.html#education", - "title": "Cait Harrigan, MSc.", - "section": "Education", - "text": "Education\n\n\n\nPhD in Computer Science, University of Toronto\n\n\nSupervised by Quaid Morris and Kieran Campbell\n\n\n\n 01/21 - present \n\n\n\n\n\nMSc. in Computer Science, University of Toronto\n\n\nSupervised by Quaid Morris\n\n\n\n 09/19 - 03/21 \n\n\n\n\n\nBSc. in Computational Biology, University of Toronto\n\n\nAwarded with distinction\n\n\n\n 09/15 - 06/19" - }, - { - "objectID": "cv_2pg.html#research-experience", - "href": "cv_2pg.html#research-experience", - "title": "Cait Harrigan, MSc.", - "section": "Research Experience", - "text": "Research Experience\n\n\n\nVisiting Graduate Researcher, Memorial Sloan Kettering Cancer Center\n\n\nHosted by Quaid Morris\n\n\n\n 06/23 - 09/23 \n\n\n\n\n\nVisiting Graduate Researcher, Memorial Sloan Kettering Cancer Center\n\n\nHosted by Quaid Morris\n\n\n\n 05/21 - 09/21 \n\n\n\n\n\nUndergraduate Research Assistant, SickKids Hospital\n\n\nSupervised by Michael Wilson and Anna Goldenberg\n\n\n\n 05/17 - 09/17" - }, - { - "objectID": "cv_2pg.html#peer-reviewed-publications", - "href": "cv_2pg.html#peer-reviewed-publications", - "title": "Cait Harrigan, MSc.", - "section": "Peer Reviewed Publications", - "text": "Peer Reviewed Publications\n* Indicates equal contribution\n\nCaitlin Timmons, Quaid Morris, and Caitlin F. Harrigan. “Regional mutational signature activities in cancer genomes”. En. In: PLOS Computational Biology 18.12 (Dec. 2022), p. e1010733.\nAgata A. Bielska, Caitlin F. Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, and Craig B. Thompson. “Activating mTOR mutations are detrimental in nutrient-poor conditions”. Eng. In: Cancer Research (Jul. 2022).\nCaitlin F. Harrigan, Yulia Rubanova, Quaid Morris, and Alina Selega. “TrackSigFreq : subclonal reconstructions based on mutation signatures and allele frequencies”. In: Pacific Symposium on Biocomputing 25 (Jan. 2020), pp. 238-249.\nYulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, and Quaid Morris. “Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig”. In: Nature Communications 11.1 (Feb. 2020), pp. 1-12." - }, - { - "objectID": "cv_2pg.html#other-publications", - "href": "cv_2pg.html#other-publications", - "title": "Cait Harrigan, MSc.", - "section": "Other Publications", - "text": "Other Publications\n\nCaitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier. “Considerations for Visualizing Uncertainty in Clinical Machine Learning Models”. Realizing AI in Healthcare: Challenges Appearing in the Wild, Workshop at CHI 2021 Online Virtual Conference, May. 2021." + "text": "I am a graduate student at the University of Toronto supervised by Quaid Morris and Kieran Campbell, and a graduate researcher at the Vector Institute and Ontario Institute for Cancer Research. I use machine learning to understand cancer evolution.\nI did my undergraduate studies at the University of Toronto, in Computational Biology and Statistics. I’m passionate about open science, and promoting great mentorship in the sciences.\nI like to drink coffee and go hiking ☕ 🏔️ ☀️" }, { - "objectID": "cv_2pg.html#fellowships-awards", - "href": "cv_2pg.html#fellowships-awards", - "title": "Cait Harrigan, MSc.", - "section": "Fellowships & Awards", - "text": "Fellowships & Awards\n\n\n\nVector Institute Research Grant\n\n\nVector Institute, Toronto, Canada\n\n\n\n 03/20 - present \n\n\n\n\n\nNSERC Postgraduate Scholarship - Doctoral\n\n\nUniversity of Toronto\n\n\n\n 09/22 - present \n\n\n\n\n\nDSI Doctoral Student Fellowship Award\n\n\nData Science Institute, University of Toronto\n\n\n\n 09/22 - present \n\n\n\n\n\nQueen Elizabeth II Graduate Scholarship in Science & Technology\n\n\n(respectfully declined)\n\n\n\n 07/22 \n\n\n\n\n\nOntario Graduate Scholarship\n\n\nDepartment of Computer Science, University of Toronto\n\n\n\n 09/21 - 09/22 \n\n\n\n\n\nACM SIGHPC Computational & Data Science Fellowship\n\n\nSpecial Interest Group on High Performance Computing of the Association for Computing Machinery\n\n\n\n 07/20 - 07/22 \n\n\n\n\n\nJXTX foundation Genome Informatics Scholarship\n\n\nJames P. Taylor Foundation for Open Science\n\n\n\n 08/21 \n\n\n\n\n\nGeneral Motors Women in Science and Mathematics Award\n\n\nUniversity of Toronto\n\n\n\n 09/20 \n\n\n\n\n\nNIH Conference Travel Fellowship\n\n\nInternational Society for Computational Biology\n\n\n\n 11/19 \n\n\n\n\n\nThe Audrey Taylor Award\n\n\nNew College, University of Toronto\n\n\n\n 07/17" + "objectID": "index.html#research", + "href": "index.html#research", + "title": "Hi, I’m Cait", + "section": "Research", + "text": "Research\n* Indicates equal contribution\n\n\n Download as BibTeX\n\nPeer Reviewed Publications\n\n\n\nRegional Mutational Signature Activities in Cancer Genomes\n\n\nCaitlin Timmons, Quaid Morris, and Caitlin F. Harrigan\n\n\nPLOS Computational Biology, 2022\n\n\n\n view code\n\n\n\n\n\nActivating mTOR mutations are detrimental in nutrient-poor conditions\n\n\nAgata A. Bielska, Caitlin F. Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, and Craig B. Thompson\n\n\nCancer Research, 2022\n\n\n\n view code\n\n\n\n\n\nReconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig\n\n\nYulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, and Quaid Morris\n\n\nNature Communications, 2020\n\n\n\n view code\n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nCaitlin F. Harrigan, Yulia Rubanova, Quaid Morris, and Alina Selega\n\n\nPacific Symposium on Biocomputing, 2020\n\n\n\n view\n\n\n\n\nOther Publications\n\n\n\nConsiderations for Visualizing Uncertainty in Clinical Machine Learning Models\n\n\nCaitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier\n\n\nWorkshop paper at CHI 2021\n\n\n\n view pdf\n\n\n\n\nPosters\n\n\n\nDirichlet allocation of mutations to model DDR in cancer\n\n\nToronto DNA Damage & Repair Symposium\n\n\n\n 04/23 \n\n\n\n\n\nDirichlet Allocation of Mutations Captures the Action of DNA Damage and Misrepair Processes\n\n\nIntelligent Systems for Molecular Biology\n\n\n\n 07/22 \n\n\n\n\n\nDirichlet Allocation of Mutations in Cancer Genomes\n\n\nMachine Learning in Computational Biology\n\n\n\n 11/21 \n\n\n\n\n\nTandem Signatures of DNA Damage and Misrepair in Cancer\n\n\nComputing Research Association’s Grad Cohort for Women\n\n\n\n 04/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nMachine Learning in Computational Biology\n\n\n\n 12/19" }, { - "objectID": "cv_2pg.html#talks", - "href": "cv_2pg.html#talks", - "title": "Cait Harrigan, MSc.", + "objectID": "index.html#talks", + "href": "index.html#talks", + "title": "Hi, I’m Cait", "section": "Talks", - "text": "Talks\n\n\n\nMutational Signatures for DNA Damage and Misrepair\n\n\nMathematical Methods in Cancer Biology, Evolution and Therapy (BIRS 23w5084)\n\n\nInvited talk\n\n\n\n 05/23 view\n\n\n\n\n\nDAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair\n\n\nCold Spring Harbour Laboratory Meeting: Genome Informatics\n\n\nSelected Talk\n\n\n\n 11/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nPacific Symposium on Biocomputing\n\n\nSelected Talk, Poster\n\n\n\n 01/20" - }, - { - "objectID": "cv_2pg.html#research-mentorship", - "href": "cv_2pg.html#research-mentorship", - "title": "Cait Harrigan, MSc.", - "section": "Research Mentorship", - "text": "Research Mentorship\n\n\n\nFedir Zhydok\n\n\nUndergraduate Student, National University of Kyiv-Mohyla Academy\n\n\nTopic: Identifying metastatic tumours from mutational signatures\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nCaitlin Timmons\n\n\nUndergraduate Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Modelling spatial distribution of mutational signatures in cancer genomes.\n\n\n\n 05/21 - 08/22 view\n\n\n\n\n\nHaritha Lakshmanan\n\n\nHighschool Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Automatic discovery of mutations predictive of survival in breast cancer patients\n\n\n\n 05/20 - 11/20 view\n\n\n\nLast updated: Nov 2023" + "text": "Talks\n\nAcademic Talks\n\n\n\nDAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair\n\n\nCold Spring Harbour Laboratory Meeting: Genome Informatics\n\n\nSelected Talk\n\n\n\n 11/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nPacific Symposium on Biocomputing\n\n\nSelected Talk, Poster\n\n\n\n 01/20 \n\n\n\n\nGuest Lectures\n\n\n\nExploring & Explaining Data in the Wild\n\n\nAI & Data Science Post-Graduate Program, Loyalist College\n\n\nInvited by Prof. Peter Papadakos\n\n\n\n 03/23 view code\n\n\n\n\n\nData Collection & Analysis\n\n\nPRISM research & mentorship program, University of Toronto\n\n\nInvited by Prof. Sadia Sharmin\n\n\n\n 02/22 pdf\n\n\n\n\n\nEnvironmental & Life Sciences Workshop Series\n\n\nSTEMHub Foundation\n\n\nInvited workshop series\n\n\n\n 01/20 \n\n\n\n\n\nR for bioinformatics\n\n\nGlobal Society for Genetics and Genome Biology\n\n\nInvited workshop\n\n\n\n 01/20 \n\n\n\n\nOther Talks\n\n\n\nFinding the ‘I’ in science\n\n\nACM Canadian Celebration of  Women in Computing\n\n\nSelected Workshop\n\n\n\n 10/22 pdf\n\n\n\n\n\nUndergraduate research opportunities: how to find them and make them work for you\n\n\nUofT Bioinformatics and Computational Biology Student Union\n\n\nInvited by the BCBSU\n\n\n\n 02/20 \n\n\n\n\n\nHow to hack your degree\n\n\nComputer Science Student Union, University of Toronto\n\n\nInvited by the CSSU\n\n\n\n 05/19" }, { - "objectID": "blog.html", - "href": "blog.html", - "title": "Cait Harrigan", - "section": "", - "text": "Order By\n Default\n \n Title\n \n \n Date - Oldest\n \n \n Date - Newest\n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\nResearch dashboard in Notion\n\n\nFree template for you <3\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nNov 29, 2023\n\n\n2 min\n\n\n\n\n\n\n \n\n\n\n\nReflection on Toronto GAAP\n\n\nApplication help for prospective graduate students\n\n\n\n\nmentorship\n\n\npassion project\n\n\n \n\n\n\n\nDec 4, 2022\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nWriting strategies for Canadian scholarships\n\n\nApplying for OGS, CGS/PGS, and the like.\n\n\n\n\ngradschool\n\n\ntips & tools\n\n\n \n\n\n\n\nOct 24, 2022\n\n\n9 min\n\n\n\n\n\n\n \n\n\n\n\nOperation Galiwatch\n\n\nA citizen science project to monitor pollinators\n\n\n\n\ncitizen science\n\n\npassion project\n\n\n \n\n\n\n\nJan 30, 2022\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nUndergraduate research at UofT\n\n\nLinks to some sweet resources and stuff to know when looking for research positions\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nNov 8, 2021\n\n\n7 min\n\n\n\n\n\n\n \n\n\n\n\nOde to Zotero\n\n\nZotero is my citation manager. I love it, here’s why.\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nSep 5, 2021\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nHow to be a good grad student\n\n\nIt’s not easy bein’ green\n\n\n\n\ngradschool\n\n\n \n\n\n\n\nMay 4, 2021\n\n\n2 min\n\n\n\n\n\n\nNo matching items" + "objectID": "index.html#teaching", + "href": "index.html#teaching", + "title": "Hi, I’m Cait", + "section": "Teaching", + "text": "Teaching\n\nResearch Mentorship\n\n\n\nKiki Zhang\n\n\nUndergraduate Student, Johns Hopkins University\n\n\nTopic: Mutational signatures in the context of branching evolution\n\n\n\n 06/23 - 08/23 view\n\n\n\n\n\nFedir Zhydok\n\n\nUndergraduate Student, National University of Kyiv-Mohyla Academy\n\n\nTopic: Identifying metastatic tumours from mutational signatures\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nCaitlin Timmons\n\n\nUndergraduate Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Modelling spatial distribution of mutational signatures in cancer genomes.\n\n\n\n 05/21 - 08/22 view\n\n\n\n\n\nHaritha Lakshmanan\n\n\nHighschool Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Automatic discovery of mutations predictive of survival in breast cancer patients\n\n\n\n 05/20 - 11/20 view\n\n\n\n\nTeaching Assistant Positions\n\n\n\nJSC370: Data Science II\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nJSC270: Data Science I\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nSTA313: Data Visualization\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nPRISM: Preparation for Research through Immersion, Skills, and Mentorship\n\n\n\n 01/22 - 05/22 \n\n\n\n\n\nJSC370: Data Science II\n\n\n\n 01/22 - 05/22 \n\n\n\n\n\nCSC197: Privacy in the Age of Big Data Collection\n\n\n\n 09/21 - 12/21 \n\n\n\n\n\nSTA4273: Minimizing Expectations\n\n\n\n 01/21 - 05/21 \n\n\n\n\n\nCSC197: Privacy in the Age of Big Data Collection\n\n\n\n 09/20 - 12/20 \n\n\n\n\n\nJSC270: Data Science I\n\n\n\n 01/20 - 05/20 \n\n\n\n\n\nCSC373: Algorithm Design, Analysis & Complexity\n\n\n\n 09/19 - 12/19 \n\n\n\n\nTestimonials\n\n“I was fortunate to work with Cait for almost a year and had a wonderful experience. She was patient, supportive, and skilled at explaining complicated concepts in biology and programming. As a mentor, she has a great sense of when to guide you through a problem and when to let you work through challenges on your own. She helped me grow as a researcher and writer and I’m grateful for everything I learned from her.”\n\n\n“As a mentor, Caitlin has greatly enhanced my ability to conduct research. She also provided valuable resources and aimed to make sure that I understood the fundamental concepts behind all the research conducted by breaking down difficult principles into easily comprehensible statements and thoughts. Additionally, she helped me find any sources of error as the research progressed. I enjoyed researching under her guidance, and I had an overall positive experience.”" }, { "objectID": "cv.html", @@ -249,104 +207,153 @@ "href": "cv.html#mentorship", "title": "Cait Harrigan, MSc.", "section": "Mentorship", - "text": "Mentorship\nAs part of my ongoing commitment to supporting students at all levels and background in engaging with computational biology, I make an effort to be available to provide guidance and resources to students, with a particular focus on creating an inclusive environment that fosters diverse perspectives and experiences. In addition to being a mentor through the organized programs listed here, I set aside ~2h/month for by-request 30 minute meetings.\n\n\n\nComputer Science Alumni Mentorship Program\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nStatistical Science Alumni Mentorship Program\n\n\n\n 10/21 - 05/22 \n\n\n\n\n\nProjectX machine learning research competition\n\n\n\n 09/20 - 02/21 \n\n\n\n\n\nHer Code Camp, Toronto Ontario\n\n\n\n 08/20 - 08/21 \n\n\n\n\n\nDepartment of Statistics Mentorship Program\n\n\n\n 10/18 - 05/19 \n\n\n\n\n\nSPROUT Peer Mentorship Program\n\n\n\n 09/16 - 05/19 \n\n\n\n\n\nNew College E-Mentorship Program\n\n\n\n 09/16 - 05/19 \n\n\n\n\nLast updated: Nov 2023" + "text": "Mentorship\nAs part of my ongoing commitment to supporting students at all levels and background in engaging with computational biology, I make an effort to be available to provide guidance and resources to students, with a particular focus on creating an inclusive environment that fosters diverse perspectives and experiences. In addition to being a mentor through the organized programs listed here, I set aside ~2h/month for by-request 30 minute meetings.\n\n\n\nComputer Science Alumni Mentorship Program\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nStatistical Science Alumni Mentorship Program\n\n\n\n 10/21 - 05/22 \n\n\n\n\n\nProjectX machine learning research competition\n\n\n\n 09/20 - 02/21 \n\n\n\n\n\nHer Code Camp, Toronto Ontario\n\n\n\n 08/20 - 08/21 \n\n\n\n\n\nDepartment of Statistics Mentorship Program\n\n\n\n 10/18 - 05/19 \n\n\n\n\n\nSPROUT Peer Mentorship Program\n\n\n\n 09/16 - 05/19 \n\n\n\n\n\nNew College E-Mentorship Program\n\n\n\n 09/16 - 05/19 \n\n\n\n\nLast updated: Dec 2023" }, { - "objectID": "index.html", - "href": "index.html", - "title": "Hi, I’m Cait", + "objectID": "blog.html", + "href": "blog.html", + "title": "Cait Harrigan", "section": "", - "text": "I am a graduate student at the University of Toronto supervised by Quaid Morris and Kieran Campbell, and a graduate researcher at the Vector Institute and Ontario Institute for Cancer Research. I use machine learning to understand cancer evolution.\nI did my undergraduate studies at the University of Toronto, in Computational Biology and Statistics. I’m passionate about open science, and promoting great mentorship in the sciences.\nI like to drink coffee and go hiking ☕ 🏔️ ☀️" + "text": "Order By\n Default\n \n Title\n \n \n Date - Oldest\n \n \n Date - Newest\n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\nResearch dashboard in Notion\n\n\nFree template for you <3\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nNov 29, 2023\n\n\n2 min\n\n\n\n\n\n\n \n\n\n\n\nReflection on Toronto GAAP\n\n\nApplication help for prospective graduate students\n\n\n\n\nmentorship\n\n\npassion project\n\n\n \n\n\n\n\nDec 4, 2022\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nXetthecum\n\n\nDigital ecocultural mapping\n\n\n\n\ncitizen science\n\n\npassion project\n\n\n \n\n\n\n\nDec 4, 2022\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nWriting strategies for Canadian scholarships\n\n\nApplying for OGS, CGS/PGS, and the like.\n\n\n\n\ngradschool\n\n\ntips & tools\n\n\n \n\n\n\n\nOct 24, 2022\n\n\n9 min\n\n\n\n\n\n\n \n\n\n\n\nOperation Galiwatch\n\n\nA citizen science project to monitor pollinators\n\n\n\n\ncitizen science\n\n\npassion project\n\n\n \n\n\n\n\nJan 30, 2022\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nUndergraduate research at UofT\n\n\nLinks to some sweet resources and stuff to know when looking for research positions\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nNov 8, 2021\n\n\n7 min\n\n\n\n\n\n\n \n\n\n\n\nOde to Zotero\n\n\nZotero is my citation manager. I love it, here’s why.\n\n\n\n\ntips & tools\n\n\n \n\n\n\n\nSep 5, 2021\n\n\n1 min\n\n\n\n\n\n\n \n\n\n\n\nHow to be a good grad student\n\n\nIt’s not easy bein’ green\n\n\n\n\ngradschool\n\n\n \n\n\n\n\nMay 4, 2021\n\n\n2 min\n\n\n\n\n\n\nNo matching items" }, { - "objectID": "index.html#research", - "href": "index.html#research", - "title": "Hi, I’m Cait", - "section": "Research", - "text": "Research\n* Indicates equal contribution\n\n\n Download as BibTeX\n\nPeer Reviewed Publications\n\n\n\nRegional Mutational Signature Activities in Cancer Genomes\n\n\nCaitlin Timmons, Quaid Morris, and Caitlin F. Harrigan\n\n\nPLOS Computational Biology, 2022\n\n\n\n view code\n\n\n\n\n\nActivating mTOR mutations are detrimental in nutrient-poor conditions\n\n\nAgata A. Bielska, Caitlin F. Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, and Craig B. Thompson\n\n\nCancer Research, 2022\n\n\n\n view code\n\n\n\n\n\nReconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig\n\n\nYulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, and Quaid Morris\n\n\nNature Communications, 2020\n\n\n\n view code\n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nCaitlin F. Harrigan, Yulia Rubanova, Quaid Morris, and Alina Selega\n\n\nPacific Symposium on Biocomputing, 2020\n\n\n\n view\n\n\n\n\nOther Publications\n\n\n\nConsiderations for Visualizing Uncertainty in Clinical Machine Learning Models\n\n\nCaitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier\n\n\nWorkshop paper at CHI 2021\n\n\n\n view pdf\n\n\n\n\nPosters\n\n\n\nDirichlet allocation of mutations to model DDR in cancer\n\n\nToronto DNA Damage & Repair Symposium\n\n\n\n 04/23 \n\n\n\n\n\nDirichlet Allocation of Mutations Captures the Action of DNA Damage and Misrepair Processes\n\n\nIntelligent Systems for Molecular Biology\n\n\n\n 07/22 \n\n\n\n\n\nDirichlet Allocation of Mutations in Cancer Genomes\n\n\nMachine Learning in Computational Biology\n\n\n\n 11/21 \n\n\n\n\n\nTandem Signatures of DNA Damage and Misrepair in Cancer\n\n\nComputing Research Association’s Grad Cohort for Women\n\n\n\n 04/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nMachine Learning in Computational Biology\n\n\n\n 12/19" + "objectID": "cv_2pg.html", + "href": "cv_2pg.html", + "title": "Cait Harrigan, MSc.", + "section": "", + "text": "Cait Harrigan, MSc.\n\ncait.harrigan@mail.utoronto.ca | View this CV online at caitharrigan.ca/cv\nI am a graduate student at the University of Toronto supervised by Quaid Morris and Kieran Campbell. I’m a graduate researcher at the Vector Institute and Doctoral Fellow at the UofT Data Sciences Institute. I use machine learning to understand cancer genomics by modelling the evolutionary constraints that underlie how mutations occur in DNA. I’m passionate about open science, and promoting great mentorship in the sciences." }, { - "objectID": "index.html#talks", - "href": "index.html#talks", - "title": "Hi, I’m Cait", + "objectID": "cv_2pg.html#education", + "href": "cv_2pg.html#education", + "title": "Cait Harrigan, MSc.", + "section": "Education", + "text": "Education\n\n\n\nPhD in Computer Science, University of Toronto\n\n\nSupervised by Quaid Morris and Kieran Campbell\n\n\n\n 01/21 - present \n\n\n\n\n\nMSc. in Computer Science, University of Toronto\n\n\nSupervised by Quaid Morris\n\n\n\n 09/19 - 03/21 \n\n\n\n\n\nBSc. in Computational Biology, University of Toronto\n\n\nAwarded with distinction\n\n\n\n 09/15 - 06/19" + }, + { + "objectID": "cv_2pg.html#research-experience", + "href": "cv_2pg.html#research-experience", + "title": "Cait Harrigan, MSc.", + "section": "Research Experience", + "text": "Research Experience\n\n\n\nVisiting Graduate Researcher, Memorial Sloan Kettering Cancer Center\n\n\nHosted by Quaid Morris\n\n\n\n 06/23 - 09/23 \n\n\n\n\n\nVisiting Graduate Researcher, Memorial Sloan Kettering Cancer Center\n\n\nHosted by Quaid Morris\n\n\n\n 05/21 - 09/21 \n\n\n\n\n\nUndergraduate Research Assistant, SickKids Hospital\n\n\nSupervised by Michael Wilson and Anna Goldenberg\n\n\n\n 05/17 - 09/17" + }, + { + "objectID": "cv_2pg.html#peer-reviewed-publications", + "href": "cv_2pg.html#peer-reviewed-publications", + "title": "Cait Harrigan, MSc.", + "section": "Peer Reviewed Publications", + "text": "Peer Reviewed Publications\n* Indicates equal contribution\n\nCaitlin Timmons, Quaid Morris, and Caitlin F. Harrigan. “Regional mutational signature activities in cancer genomes”. En. In: PLOS Computational Biology 18.12 (Dec. 2022), p. e1010733.\nAgata A. Bielska, Caitlin F. Harrigan, Yeon Ju Kyung, Quaid Morris, Wilhelm Palm, and Craig B. Thompson. “Activating mTOR mutations are detrimental in nutrient-poor conditions”. Eng. In: Cancer Research (Jul. 2022).\nCaitlin F. Harrigan, Yulia Rubanova, Quaid Morris, and Alina Selega. “TrackSigFreq : subclonal reconstructions based on mutation signatures and allele frequencies”. In: Pacific Symposium on Biocomputing 25 (Jan. 2020), pp. 238-249.\nYulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, and Quaid Morris. “Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig”. In: Nature Communications 11.1 (Feb. 2020), pp. 1-12." + }, + { + "objectID": "cv_2pg.html#other-publications", + "href": "cv_2pg.html#other-publications", + "title": "Cait Harrigan, MSc.", + "section": "Other Publications", + "text": "Other Publications\n\nCaitlin F. Harrigan*, Gabriella Morgenshtern*, Anna Goldenberg, and Fanny Chevalier. “Considerations for Visualizing Uncertainty in Clinical Machine Learning Models”. Realizing AI in Healthcare: Challenges Appearing in the Wild, Workshop at CHI 2021 Online Virtual Conference, May. 2021." + }, + { + "objectID": "cv_2pg.html#fellowships-awards", + "href": "cv_2pg.html#fellowships-awards", + "title": "Cait Harrigan, MSc.", + "section": "Fellowships & Awards", + "text": "Fellowships & Awards\n\n\n\nVector Institute Research Grant\n\n\nVector Institute, Toronto, Canada\n\n\n\n 03/20 - present \n\n\n\n\n\nNSERC Postgraduate Scholarship - Doctoral\n\n\nUniversity of Toronto\n\n\n\n 09/22 - present \n\n\n\n\n\nDSI Doctoral Student Fellowship Award\n\n\nData Science Institute, University of Toronto\n\n\n\n 09/22 - present \n\n\n\n\n\nQueen Elizabeth II Graduate Scholarship in Science & Technology\n\n\n(respectfully declined)\n\n\n\n 07/22 \n\n\n\n\n\nOntario Graduate Scholarship\n\n\nDepartment of Computer Science, University of Toronto\n\n\n\n 09/21 - 09/22 \n\n\n\n\n\nACM SIGHPC Computational & Data Science Fellowship\n\n\nSpecial Interest Group on High Performance Computing of the Association for Computing Machinery\n\n\n\n 07/20 - 07/22 \n\n\n\n\n\nJXTX foundation Genome Informatics Scholarship\n\n\nJames P. Taylor Foundation for Open Science\n\n\n\n 08/21 \n\n\n\n\n\nGeneral Motors Women in Science and Mathematics Award\n\n\nUniversity of Toronto\n\n\n\n 09/20 \n\n\n\n\n\nNIH Conference Travel Fellowship\n\n\nInternational Society for Computational Biology\n\n\n\n 11/19 \n\n\n\n\n\nThe Audrey Taylor Award\n\n\nNew College, University of Toronto\n\n\n\n 07/17" + }, + { + "objectID": "cv_2pg.html#talks", + "href": "cv_2pg.html#talks", + "title": "Cait Harrigan, MSc.", "section": "Talks", - "text": "Talks\n\nAcademic Talks\n\n\n\nDAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair\n\n\nCold Spring Harbour Laboratory Meeting: Genome Informatics\n\n\nSelected Talk\n\n\n\n 11/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nPacific Symposium on Biocomputing\n\n\nSelected Talk, Poster\n\n\n\n 01/20 \n\n\n\n\nGuest Lectures\n\n\n\nExploring & Explaining Data in the Wild\n\n\nAI & Data Science Post-Graduate Program, Loyalist College\n\n\nInvited by Prof. Peter Papadakos\n\n\n\n 03/23 view code\n\n\n\n\n\nData Collection & Analysis\n\n\nPRISM research & mentorship program, University of Toronto\n\n\nInvited by Prof. Sadia Sharmin\n\n\n\n 02/22 pdf\n\n\n\n\n\nEnvironmental & Life Sciences Workshop Series\n\n\nSTEMHub Foundation\n\n\nInvited workshop series\n\n\n\n 01/20 \n\n\n\n\n\nR for bioinformatics\n\n\nGlobal Society for Genetics and Genome Biology\n\n\nInvited workshop\n\n\n\n 01/20 \n\n\n\n\nOther Talks\n\n\n\nFinding the ‘I’ in science\n\n\nACM Canadian Celebration of  Women in Computing\n\n\nSelected Workshop\n\n\n\n 10/22 pdf\n\n\n\n\n\nUndergraduate research opportunities: how to find them and make them work for you\n\n\nUofT Bioinformatics and Computational Biology Student Union\n\n\nInvited by the BCBSU\n\n\n\n 02/20 \n\n\n\n\n\nHow to hack your degree\n\n\nComputer Science Student Union, University of Toronto\n\n\nInvited by the CSSU\n\n\n\n 05/19" + "text": "Talks\n\n\n\nMutational Signatures for DNA Damage and Misrepair\n\n\nMathematical Methods in Cancer Biology, Evolution and Therapy (BIRS 23w5084)\n\n\nInvited talk\n\n\n\n 05/23 view\n\n\n\n\n\nDAMUTA: Dirichlet allocation of mutations as a function of both damage and DNA repair\n\n\nCold Spring Harbour Laboratory Meeting: Genome Informatics\n\n\nSelected Talk\n\n\n\n 11/21 \n\n\n\n\n\nTrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies\n\n\nPacific Symposium on Biocomputing\n\n\nSelected Talk, Poster\n\n\n\n 01/20" }, { - "objectID": "index.html#teaching", - "href": "index.html#teaching", - "title": "Hi, I’m Cait", - "section": "Teaching", - "text": "Teaching\n\nResearch Mentorship\n\n\n\nKiki Zhang\n\n\nUndergraduate Student, Johns Hopkins University\n\n\nTopic: Mutational signatures in the context of branching evolution\n\n\n\n 06/23 - 08/23 view\n\n\n\n\n\nFedir Zhydok\n\n\nUndergraduate Student, National University of Kyiv-Mohyla Academy\n\n\nTopic: Identifying metastatic tumours from mutational signatures\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nCaitlin Timmons\n\n\nUndergraduate Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Modelling spatial distribution of mutational signatures in cancer genomes.\n\n\n\n 05/21 - 08/22 view\n\n\n\n\n\nHaritha Lakshmanan\n\n\nHighschool Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Automatic discovery of mutations predictive of survival in breast cancer patients\n\n\n\n 05/20 - 11/20 view\n\n\n\n\nTeaching Assistant Positions\n\n\n\nJSC370: Data Science II\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nJSC270: Data Science I\n\n\n\n 01/23 - 05/23 \n\n\n\n\n\nSTA313: Data Visualization\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nPRISM: Preparation for Research through Immersion, Skills, and Mentorship\n\n\n\n 01/22 - 05/22 \n\n\n\n\n\nJSC370: Data Science II\n\n\n\n 01/22 - 05/22 \n\n\n\n\n\nCSC197: Privacy in the Age of Big Data Collection\n\n\n\n 09/21 - 12/21 \n\n\n\n\n\nSTA4273: Minimizing Expectations\n\n\n\n 01/21 - 05/21 \n\n\n\n\n\nCSC197: Privacy in the Age of Big Data Collection\n\n\n\n 09/20 - 12/20 \n\n\n\n\n\nJSC270: Data Science I\n\n\n\n 01/20 - 05/20 \n\n\n\n\n\nCSC373: Algorithm Design, Analysis & Complexity\n\n\n\n 09/19 - 12/19 \n\n\n\n\nTestimonials\n\n“I was fortunate to work with Cait for almost a year and had a wonderful experience. She was patient, supportive, and skilled at explaining complicated concepts in biology and programming. As a mentor, she has a great sense of when to guide you through a problem and when to let you work through challenges on your own. She helped me grow as a researcher and writer and I’m grateful for everything I learned from her.”\n\n\n“As a mentor, Caitlin has greatly enhanced my ability to conduct research. She also provided valuable resources and aimed to make sure that I understood the fundamental concepts behind all the research conducted by breaking down difficult principles into easily comprehensible statements and thoughts. Additionally, she helped me find any sources of error as the research progressed. I enjoyed researching under her guidance, and I had an overall positive experience.”" + "objectID": "cv_2pg.html#research-mentorship", + "href": "cv_2pg.html#research-mentorship", + "title": "Cait Harrigan, MSc.", + "section": "Research Mentorship", + "text": "Research Mentorship\n\n\n\nFedir Zhydok\n\n\nUndergraduate Student, National University of Kyiv-Mohyla Academy\n\n\nTopic: Identifying metastatic tumours from mutational signatures\n\n\n\n 09/22 - 12/22 \n\n\n\n\n\nCaitlin Timmons\n\n\nUndergraduate Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Modelling spatial distribution of mutational signatures in cancer genomes.\n\n\n\n 05/21 - 08/22 view\n\n\n\n\n\nHaritha Lakshmanan\n\n\nHighschool Student, Memorial Sloan Kettering Cancer Center\n\n\nTopic: Automatic discovery of mutations predictive of survival in breast cancer patients\n\n\n\n 05/20 - 11/20 view\n\n\n\nLast updated: Dec 2023" }, { - "objectID": "posts/2021-09-05-ode-to-zotero/index.html", - "href": "posts/2021-09-05-ode-to-zotero/index.html", - "title": "Ode to Zotero", + "objectID": "posts/2021-05-04-how-to-be-a-good-grad-student/index.html", + "href": "posts/2021-05-04-how-to-be-a-good-grad-student/index.html", + "title": "How to be a good grad student", "section": "", - "text": "Zotero is my citation manager. I love it, here’s why.\n\nIt’s open source\nIt’s lightweight\nIt syncs with overleaf\nIt has excellent search\nOne click to save from browser\nIt syncs to the cloud\nCustomizable bibliography formats\n\nMore reasons to love:\n\nLots of free storage\nIntegreations with Word, Google docs, etc\nThe project folders are great for organizing research\nAutomatic report generation with all your notes\nGroup-libraries for collaboration\nA cute timeline generator\n\n\n\n\nYou can see I got excited about genomics around 2017." + "text": "Over the last year, I asked several of my mentors this question:\n\nWhat makes for a truly excellent grad student?\n\nI highly recommend you put this question to the people in your life that you work with, and admire. So far, I’ve received several thoughtful answers, but the question often seems to takes people by surprise. This seems funny to me and it made me realize that although a lot of grad students seem to be concerned with “am I doing a good job?” they aren’t asking for help on how to do a good job.\n\n\nObviously you can substitute “grad student” with whatever your current position is. I think this is a valuable question in general for getting perspective on what skills and behaviours you should be investing your time into.\nHere are some of my favourite responses:\n\nThey read a lot. They survey the field and have a good understanding of what’s out there and how their work fits within the context of the research landscape, and how their work is driving the field forward.\nThey are someone who focuses on what the big-picture impact of their project is, and thinks about the ultimate results and their significance.\nThey are a good communicator. They can write clearly, and they can explain their ideas.\nThey know how to make use of their advisor. Often, there are things that an advisor knows a simple answer to, that students don’t find out about just because they didn’t ask." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html", - "title": "Undergraduate research at UofT", + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html", + "title": "Writing strategies for Canadian scholarships", "section": "", - "text": "This post is aimed primarily at students interested in computational biology and machine learning, but not restricted to these areas by any means." + "text": "This post is my attempt to compile what I’ve learned about writing though applying for government scholarships. Most of it comes from my own trial and error, but some I also picked up from workshops1, and by looking at other people’s proposals 2.\nDisclaimer: I’m not a writer by training, and I definitely haven’t won all the awards I’ve ever applied to. This is really just a list of things that I wish I knew the first time I applied to government scholarships. All the following tips are aimed at building technical project proposals, with a bias towards NSERC because that’s the agency that my work falls under." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#resources", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#resources", - "title": "Undergraduate research at UofT", - "section": "Resources", - "text": "Resources\nBefore I say anything at all, I must promote the excellent advice that others have compiled.\nThis is a small selection of my personal favourites, but many of them link out to even more resources.\n\nReview of Undergraduate Computer Science (RUCS) and their fabulous Undergraduate Research Guide\nThe Bioinformatics and Computational Biology Student Union (BCBSU) hosts and annual information session on research courses BCB330 & BCB430\nTips on finding a supervisor from the BCB program" + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#general-advice", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#general-advice", + "title": "Writing strategies for Canadian scholarships", + "section": "General advice", + "text": "General advice\n\nUse a citation manager\nIf you’re not already using a citation management tool, then your life is harder than it needs to be. I use Zotero, but some people prefer Mendeley, or Paperpile, for example.\n\n\nI explain all the reasons I love Zotero here.\n\n\nDon’t expect to nail it on the first try.\nA common theme seems to be “I didn’t get any awards at all at first, then something clicked and I seemed to get them all at once”. You will probably have to apply several years in a row before you have a good grasp on the language to use to describe your problem, and build a strong understand where your work fits within the field as a whole.\nLuckily, the easiest thing to work off of is your own past writing. If you start early, you will become a valuable resource to your future self 😁\n\n\nGet writing help\nMany universities have a writing center, with workshops aimed at specific scholarships. Look into their calendar ahead of time, as you’ll get the most out of it if you can bring a draft with you.\n\n\nGet someone else to read it\nBonus points if they are not in your field, and are able to grasp your research proposal enough to get excited about your problem. This is a good litmus test for writing clarity." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#research-comes-in-many-shapes-and-sizes", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#research-comes-in-many-shapes-and-sizes", - "title": "Undergraduate research at UofT", - "section": "Research comes in many shapes and sizes", - "text": "Research comes in many shapes and sizes\nUniversity of Toronto is part of a rich research ecosystem in Toronto, and if you want to try out research as an undergrad, this is a great place to do it! In addition the University labs, many professors from associated institutes are able to take on UofT students for research. To name a few:\n\nUnited Health Netowrk\nSickKids Hospital\nLunenfeld-Tanenbaum Research Institute\nOntario Insitute for Cancer Research\nData Sciences Insitute\nVector Institute\n\nAs an undergrad, I was in the Bioinformatics and Computational Biology program 2015-2019. As part of the requirements for that program, I took two research project courses; BCB330 and BCB430. There are many similar courses offered through a variety of programs, such as ROPs, capstone projects, independent research projects, etc. Most of these are blank-cheque style courses you get credit for by working with a professor in a research capacity.\nSometimes you can get a paid research position supported by a USRA grant. These are grants offered by the Canadian government to encourage labs to hire undergraduate students for summer research positions.\n\n\n\n\n\n\nNote\n\n\n\nDon’t apply on your own! The USRA proposal expectations are particular, and field-specific. Ask your professor or research mentor for help with crafting the application.\n\n\n\nCourse-based programs\nOften, you don’t strictly have to be enrolled in a program to take their research course. You can inquire into research offerings in programs such as CSC, STA, BCB, MGY, BCH, CSB, MBP, and more.\n\n\nSummer programs\nA few examples listed here, by no means exhaustive.\n\nDonnelly Center summer studentships\nVector internships\nTCAIREM summer studentships\nDSI Summer Undergraduate Data Science (SUDS) Opportunities Program" + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#an-algorithm-to-write-to", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#an-algorithm-to-write-to", + "title": "Writing strategies for Canadian scholarships", + "section": "An algorithm to write to", + "text": "An algorithm to write to\nI use this same process for both technical writing, and personal statements. This is what works for me personally: take what you like and ignore the rest 😊\n\n\n\n\n\n\nWarning\n\n\n\nI am writing this in 2022. The specific formatting instructions might have changed since then. Never listen to anyone about presentation standards, except the official instructions.\n\n\nDo the following things in this order:\n\nSet up page margins to 2cm\nSet font to 12pt Arial\nWrite the title and your name in the header. Don’t forget to paginate where appropriate.\nPaste the instructions into the document, anything that gives guidelines on what the content should be. Check back on these as you write, especially if you get stuck on what to write about.\nWrite a bullet point outline of all the ideas you want to include (past/present/future work, practical implementation, etc)\nWrite statement-style headers for each section, in a way that captures the narrative flow of the story. These headers should be written such that they are sufficient that someone reading them could explain your whole project, even though you haven’t written the content yet. Put them in bold.\nAssign the bullet points to headers. These will guide how you flush out the body text.\nWrite the content paragraphs. Don’t worry about writing them in order. If you have trouble making progress on one, write a brief skeleton the best you can, and move on to a different section. The headers from step 5 will give you a strong sense of which chunks of text are self-contained.\nEdit. Go back to any paragraphs that are not flowing correctly. Use a read-aloud service (ex. in Word) to listen to your draft.\nRealize you’re about 20% over the page limit. Change font to 12pt Times New Roman. Now you’re done.\n\n\n\nSteps 5 & 6 should only contain sentence fragments and ideas that are easy to write. Do not spend time agonizing over wording in these steps.\n\n\n\n\n\nI learned #6 by reading other people’s examples. Done correctly, your headers will greatly improve readability. Ultimately you want your writing to be as skimmable as possible. This is important, because your application will be one of a large number of others that reviewers will have to read through.\n#10 is also a critical trick for me: always draft in Arial before finalizing to Times New Roman. TNR is much more condensed, and this font conversion will gift you extra space, as long as you don’t start by writing in it. I tend to over-write, and this trick helps me avoid having to spend a lot of time cutting content.\nWhen it comes to getting the exact wording you want, don’t let perfect be the enemy of progress. When you get stuck on a word:\n\nUse a thesaurus\nLook at other writing samples (some of mine are available here)\nWrite down a few synonyms of the word you’re trying to find as a note to self and come back to it later." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#dont-work-for-free", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#dont-work-for-free", - "title": "Undergraduate research at UofT", - "section": "Don’t work for free!", - "text": "Don’t work for free!\nI’ll say it again: don’t work for free!\nYou should either get course credit, or a paycheck for your time. (If you can swing it, get both!) Don’t underestimate the value of your contributions as an undergraduate researcher.\nI hate to see students being taken advantage of via “laboratory volunteer” positions. For one thing, unpaid internships are not legal in Canada.\nIt’s also a big red flag that your work is not being valued as it should be. Chances are that there is a more suitable position out there for you that will serve you better, and compensate you fairly. “Potentially” getting authorship on a publication is not payment." + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#ogs-cgspgs-specific-advice", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#ogs-cgspgs-specific-advice", + "title": "Writing strategies for Canadian scholarships", + "section": "OGS & CGS/PGS specific advice", + "text": "OGS & CGS/PGS specific advice\nI have used more or less the same structure for my successful award applications3:\n\nOGS 2021\nPGS-D 2021\nQEII-GSST 2022\nDSI fellowship 2022\n\n\nStructure of the research proposal\n\n\n\n\n\n\nNote\n\n\n\nThis is just one structuring example which I have followed. Don’t feel bound to what I describe here, if your writing heart leads you elsewhere\n\n\nThere are a few points in this structure that are subtly distinct. You should not just paraphrase the same sentence twice for these, which is a pitfall I’ve run into. I have highlighted pairs of elements in this structure should not get conflated, because these elements have different roles in the proposal. Distinguish them from each other by changing the scope of what you describe.\n\nBackground and motivation\n\nWhere we are now (state of the field)\nWhat’s needed (key steps in new knowledge generation)\n\nObjectives and hypothesis\n\nWhat you’re developing (one-liner)\nWhat it will enable (big picture impact of your results)\n\nKnowledge gap (The direction your results will take the field in. Keep it large enough scale/scope that your project does not completely fill this gap, but maybe your project, plus 3-5 years more research would.)\nSignificance (Implications of what your project will enable)\nExperimental and theoretical approach\n\nSummary of 2-3 goals. Goals should describe the overarching themes of what your results will show.\n2-3 aims, with substeps that build to each aim. Aims should be actionable steps you will take, and build on each other logically, however later aims should not strictly rely on the success of earlier aims in order to be possible to execute. (What would you do if the early stuff didn’t work out? You don’t want to leave your proposal vulnerable to that question.)\n\nWhy you are uniquely positioned to execute the research here and now\n\n\n\nPitfalls\nThe biggest challenge for new grad students is not yet having a strong grasp on the state of their field, and how their project fits in that context.\n\nProbably your PI has a good idea of this, and your lab may have an overarching research story that you can tap into. Ask you PI for writing advice!\nThe only other thing you can do to improve on this is to read widely and engage with other researchers in your field. This is more of a student-lifestyle thing than it is writing advice, but it makes for a good researcher (and subsequently, research proposal).\n\n\n\nResearch contributions\nYour research contributions should include everything you did. This also means things that you had shared responsibility with others. (ex. put down writing if you wrote part of the original draft, even if someone else also wrote part). I recommend referring to CRediT taxonomy for a list and description of roles.\n\n\nRelevant Activities\nI treated this section as place to highlight my non-research CV items. They should ideally have some tie-in to your career goals, and speak to your attributes as a researcher. See Create a draft that harmonizes with your reference letters below." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#choose-a-lab", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#choose-a-lab", - "title": "Undergraduate research at UofT", - "section": "Choose a lab", - "text": "Choose a lab\nMost departments have a list of faculty, this is a good place to start. Survey the landscape of professors that you might work with by looking at their google scholar profile. An easy way to find other similar labs is to click through their co-authors.\nFor an interdisciplinary field such as computational biology, I found it useful to look through the faculty pages of multiple departments, various hospital labs, and start-ups that I knew my peers had done research or PEY at.\n\nCold contacting\nThere are many resources out there for how to compose the dreaded “cold email”, some that I’ve linked to above. Briefly, here is the anatomy of the cold emails I have sent:\n\nintroduce yourself\nexplain what kind of position your looking for\nmention one thing in their recent publication record or lab website that made their research stick out to you\ndescribe any relevant past experience you have\nask for an interview\nattach a cover letter (optional, the email itself may serve as this)\nattach your CV\nattach your transcripts\n\n\n\n\n\n\n\nTip\n\n\n\nAttach your transcripts even if you’re not happy with your grades (I certainly felt this way!) This will increase the likelihood that you hear back and make things go faster. The grades themselves are often not particularly important, but attaching the transcript is a simple way to indicate that you understand what this type of email should contain.\n\n\n\n\n\n\n\n\nTip\n\n\n\nProfessors are generally very busy and terrible at responding to emails. Send a few out to different people, and if you don’t hear back from anyone after about a week, follow up or move on. Radio silence is common, so don’t be discouraged by it." + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#reference-letters", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#reference-letters", + "title": "Writing strategies for Canadian scholarships", + "section": "Reference letters", + "text": "Reference letters\n\nOffer to draft your referee’s letters for them\nThis will make it a lot easier for your referees to agree to be a reference for you. It will also let you have a hand in what your letters look like, and ensure that they highlight the same strengths you show in the rest of the application.\nAt the very least, you should provide your references a few bullet points to work with.\n\n\nCreate a draft that harmonizes with your reference letters\nA common recipe that I have noticed in the successful applications that I’ve seen (and tried to model in my own application) to prove that your leadership is “above and beyond” goes along these lines:\n\nYou have a series of examples of times you were in a leadership position, and did something extra\n\nYou made the leadership position your own in some way\nYou took an active role in supporting others\nYou created something new to solve a problem\n\nBetween your two reference letters, all the examples you listed are repeated, but discussed from a different perspective\nYour referees identify the impact of the “something extra” that you did\nYour referees are able to explain why what you did made others admire/respect/be grateful to you\nYour referees have a lot of positive adjectives to describe your character" }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#what-to-expect-in-the-research-environment", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#what-to-expect-in-the-research-environment", - "title": "Undergraduate research at UofT", - "section": "What to expect in the research environment", - "text": "What to expect in the research environment\nI divide labs into two categories: Hands-on PI / Hands-off PI\nA Hands-on PI is a professor who has a lot of time for you, but may have high expectations on your research output. Although you may be working with a grad student, this PI could be directly involved in your project and giving you guidance. This environment might be stressful, but you’ll probably learn a lot. Watch out for unreasonable demands.\nHands-off PI has seen it all. Their group is large, and they might not make time to meet with you. They are less obviously invested in your success, but there may be less pressure on you because of this. A grad student is your direct supervisor, and you may work closely with them on their research. In this environment you will have more autonomy, but you will have to be proactive in order to learn. Watch out for feeling isolated or forgotten.\nObviously the Hands-on PI / Hands-off PI labels are not all-encompassing, and most people will fall somewhere in between the two caricatures. Every environment will have its own peculiarities, advantages, and challenges.\nIn all cases you will most likely have a chance to interact with grad students or technical staff. You will get to attend group meetings (usually weekly), and possibly be expected to present your work to the lab at group meeting." + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#leave-a-full-day-for-formatting", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#leave-a-full-day-for-formatting", + "title": "Writing strategies for Canadian scholarships", + "section": "Leave a full day for formatting", + "text": "Leave a full day for formatting\nDo not underestimate the time sink that is uploading all your files, reuploading, editing the CCV because of a missing comma, reuploading, now there’s an extra comma, reuploading, etc.\nThe first time you put everything into the CCV system is the most painful.\nAfter that it is easier :)" }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#how-are-research-courses-graded", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#how-are-research-courses-graded", - "title": "Undergraduate research at UofT", - "section": "How are research courses graded?", - "text": "How are research courses graded?\nIn general the grading for research project courses is relatively lax. Often there is a performance evaluation that your supervisor has to fill out at the end, plus some written or presentation-based deliverable for you to submit.\nMany labs will grade you based on your improvement, and you’ll get a good grade as long as you show up regularly and put effort in to learning." + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#vanier", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#vanier", + "title": "Writing strategies for Canadian scholarships", + "section": "Vanier", + "text": "Vanier\nVanier is a different beast. There is a heavy emphasis on leadership, and the expectations are not the same as CGS. Preparing a Vanier application is more work than CGS, and takes more time.\nSilvia Sellán has generously shared advice and examples from her application - which I recommend reading." }, { - "objectID": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#your-research-output", - "href": "posts/2021-11-08-undergraduate-research-at-uoft/index.html#your-research-output", - "title": "Undergraduate research at UofT", - "section": "Your research output", - "text": "Your research output\nThere are several undergraduate poster days run by various departments, often associated with their respective project courses.\nMost of the summer programs I mentioned above have their own dedicated “research day” at the end of the summer.\nIf this kind of poster day isn’t available to you, one thing you can do at the end of a research experience is to submit to an undergraduate journal or conference. Leave a couple weeks at the end of your research experience for developing a write-up or poster, and ask your mentor for input. With an end product that you deliver in someway to an audience, you will gain more out of your experience, and make it easier to put on your CV.\nSome examples of research-focused UofT student publications:\n\nArbor Journal of Undergraduate Research (The ASSU also hosts an annual undergraduate research conference)\nJULS Journal of Undergraduate Life\nRUCS Review of Undregraduate Computer Science\n\nYou can also apply to have your research appear in similar venues at other universities, or if you’re particularly ambitious, grab some friends and host your own research day 🌈" + "objectID": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#footnotes", + "href": "posts/2021-10-24-writing-strategies-for-government-scholarships/index.html#footnotes", + "title": "Writing strategies for Canadian scholarships", + "section": "Footnotes", + "text": "Footnotes\n\n\nShout-out to Daniel Newman↩︎\nSpecial thanks to SG, SS, AD, TS, JW, and SK for helpful advice they’ve shared with me.↩︎\nOf course, I’ve also used it on applications which were ultimately unsuccessful: CGS-M 2019, CGS-D 2020, Vanier 2020, Vanier 2021. However, I’d like to believe that I improved my writing skill over time, and this resulted in my later success.↩︎" }, { - "objectID": "posts/2022-12-04-GAAP/index.html", - "href": "posts/2022-12-04-GAAP/index.html", - "title": "Reflection on Toronto GAAP", + "objectID": "posts/2022-01-30-galiwatch/index.html", + "href": "posts/2022-01-30-galiwatch/index.html", + "title": "Operation Galiwatch", "section": "", - "text": "It’s my second time organizing the Toronto CS Graduate Application Assistance Program and it was a great experience!\nThe program matches current Computer Science graduate students with prospective students, with a focus for those who are underrepresented in computing. We were able to provide application feedback to 55 mentees.\nBig thanks to the volunteers for their work 🌻 we got lots of positive coments and grateful messages from mentees.\nI’m looking forward to running this program again next year!" + "text": "My parents got into birdwatching… at scale. They’ve set out to thoroughly document what’s going on in their yard on Galiano Island, BC: Operation Galiwatch.\nWe’ve set up a bunch of sensors to collect air quality data, weather information, and timelapse images. We’re monitoring all sorts of pollinators, such as bees and humming birds. If all goes well with the infrared camera, maybe even bats.\nI’ve been helping debug the setup, doing data analysis, and maintaining the Galiwatch website.\nWe’re collaborating with the folks at Biodiversity Galiano and IMERSS to make low-cost, hyperlocal ecosystem and climate monitoring accessible for other citizen scientists!" + }, + { + "objectID": "posts/2023-11-29-notion-research-dashboard/index.html", + "href": "posts/2023-11-29-notion-research-dashboard/index.html", + "title": "Research dashboard in Notion", + "section": "", + "text": "I use notion to organize lots of things, in particular my research notes. I used to use R Markdown, which was great for mixing text, images, \\(\\LaTeX\\), code, and (most importantly) emojis. However, over time my research notebook got bloated and trying to keep notes and also make sure everything rendered correctly became challenging.\nI moved to Notion because it offers a very similar experience for markdown lovers.\nPeep my template here!" + }, + { + "objectID": "posts/2023-11-29-notion-research-dashboard/index.html#thoughts-on-the-experience", + "href": "posts/2023-11-29-notion-research-dashboard/index.html#thoughts-on-the-experience", + "title": "Research dashboard in Notion", + "section": "Thoughts on the experience", + "text": "Thoughts on the experience\nHere’s some things I like about it:\n\nCloud backed + mobile app\nAll my notes are searchable\nPossible to export as markdown\nDatabases! Every page can be a database and it’s pretty cool\nTemplates! I use the “new experiment” button to add structured entries to my lab notebook\nEvery page can be reformatted and nested on the fly\nI can sync TODOs across multiple pages: my main planner, and each project’s respective TODO list\nUseful shortcuts for Today’s date and cross referencing other pages\nThere are some cute templates out there\n\nAnd some gripes:\n\nNo offline mode - even for simple notes!\nSearch UI is not great: can’t search within code chunks, or toggle sections\nMarkdown exports are clunky and not everything will be well preserved (especially images)\nAdmiring cute templates feels productive, but it’s actually a massive time sink" } ] \ No newline at end of file