├── .gitignore ├── authorship.md ├── coding-standards.md ├── how-to-craft-belonging.md ├── interest-in-lab.md ├── lab-guidelines.md ├── lit-review.md ├── lor-guidelines.md ├── on-off-boarding.md ├── postdoc-guidelines.md ├── project-plan.md ├── readme.md ├── resources.md └── things2know.md /.gitignore: -------------------------------------------------------------------------------- 1 | # Here 2 | resources/* 3 | not-public/* 4 | 5 | # Compiled source # 6 | ################### 7 | *.com 8 | *.class 9 | *.dll 10 | *.exe 11 | *.o 12 | *.so 13 | 14 | # Packages # 15 | ############ 16 | # it's better to unpack these files and commit the raw source 17 | # git has its own built in compression methods 18 | *.7z 19 | *.dmg 20 | *.gz 21 | *.iso 22 | *.jar 23 | *.rar 24 | *.tar 25 | *.zip 26 | 27 | # Logs and databases # 28 | ###################### 29 | *.log 30 | *.sql 31 | *.sqlite 32 | 33 | # OS generated files # 34 | ###################### 35 | .DS_Store 36 | .DS_Store? 37 | ._* 38 | .Spotlight-V100 39 | .Trashes 40 | ehthumbs.db 41 | Thumbs.db 42 | 43 | # from tex files # 44 | ################# 45 | *.aux 46 | *.glo 47 | *.idx 48 | *.log 49 | *.toc 50 | *.ist 51 | *.acn 52 | *.acr 53 | *.alg 54 | *.bbl 55 | *.blg 56 | *.dvi 57 | *.glg 58 | *.gls 59 | *.ilg 60 | *.ind 61 | *.lof 62 | *.lot 63 | *.maf 64 | *.mtc 65 | *.mtc1 66 | *.synctex.gz 67 | *.pdf 68 | *.bst 69 | 70 | 71 | # Mac IDE files 72 | *.swp 73 | *~ 74 | *(Autosaved).rtfd/ 75 | Backup[ ]of[ ]*.pages/ 76 | Backup[ ]of[ ]*.key/ 77 | Backup[ ]of[ ]*.numbers/ 78 | 79 | 80 | # julia or R 81 | *.juliahistory 82 | *.Rhistory 83 | *.err 84 | *.RData 85 | *.Rda 86 | *.rds 87 | *.jld 88 | *.Rproj* 89 | *.Ruserdata 90 | 91 | # open office 92 | *.odt 93 | *.csv 94 | 95 | # inkscape drawings 96 | *.svg 97 | *.eps 98 | *.jpg 99 | *.jpeg 100 | *.png 101 | *.dot 102 | *.json 103 | 104 | # dropbox 105 | .dropbox 106 | 107 | # keynote 108 | *.key 109 | 110 | ### office 111 | *.xls* 112 | *.doc* 113 | *.ppt* 114 | 115 | 116 | ### plink 117 | *.raw 118 | *.bed 119 | *.bim 120 | *.fam 121 | *.ped 122 | *.map 123 | *.frq 124 | *.imiss 125 | *.lmiss 126 | *.vcf 127 | *.tsv 128 | *.cov 129 | *.dosage 130 | *.prob 131 | *.freq 132 | *.nosex 133 | 134 | ## html 135 | *.html 136 | *.css 137 | *.js 138 | *.ttf 139 | 140 | ### sequences 141 | *.aln 142 | *.fna 143 | *.faa 144 | *.fasta 145 | *.fa 146 | *.dat 147 | *.paml 148 | 149 | ### Mathematica 150 | *.nb -------------------------------------------------------------------------------- /authorship.md: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | pdf_document: default 4 | html_document: default 5 | --- 6 | # Authorship guidelines in the Solis-Lemus lab 7 | 8 | - The trainee (student/postdoc in the lab) taking the lead role can expect to be the first author of published work 9 | - Others who help over the course of the project will have the opportunity to earn co-authorship 10 | - We are open to collaborations with equal contributions and first co-authorship 11 | - The first author is responsible for: 12 | - Writing the [project plan](https://github.com/solislemuslab/lab-dynamics/blob/master/project-plan.md) (often in collaboration with other members of the research team) 13 | - Leading the project 14 | - Conducting all analyses 15 | - Writing the manuscript 16 | - Revising the manuscript and corresponding with the journal or publisher 17 | - Obtaining approval of all coauthors on the final draft 18 | - Understanding the general principles of all the work included in the manuscript. 19 | - Claudia will be the senior author (last author) and corresponding author 20 | - Being last and corresponding author signals that this is a paper from the Solis-Lemus lab 21 | - The senior author’s responsibility is 22 | - to guide the trainee’s analyses, 23 | - to provide detailed feedback on all aspects of the work (analyses, presentation of results, writing) and 24 | - to conduct careful editing of the draft prepared by the trainee before it can be sent out for publication 25 | - Claudia makes the final decision on authorship and readiness for publication. All authorship is tentative until acceptance 26 | - Discussing authorship at the start of a project is just a start as things can change 27 | - During drafting, the paper can have simply a primary author (trainee) and senior author (Claudia) with the understanding at that point that even the primary authorship is not defined until the scope of the research contained, and the manuscript is actually at the submission stage 28 | - Please feel free to bring up questions about authorship with Claudia at any point 29 | - If you leave the lab with unpublished work, you should talk to Claudia about plans to finish, submit, and revise. This may include revisiting authorship. 30 | - We aim to publish all papers from the lab on pre-print servers such as arxiv and bioarxiv 31 | - All abstracts, posters, talks, preprints and papers are representations of the lab and must be approved by Claudia before submission 32 | 33 | 34 | Name of trainee: 35 | 36 | Signature of trainee: 37 | 38 | Date: -------------------------------------------------------------------------------- /coding-standards.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Suggestions and Best Practices for Coding in Teams" 3 | collection: posts 4 | permalink: /blog/team_coding 5 | --- 6 | 7 | Working in a team can be an incredibly effective way to develop a package or application. However, working in a team comes with its own challenges not faced when working alone. Below are lessons I've learned the hard way from working on team-based projects. 8 | 9 | # Before Starting 10 | 11 | 1. Map out the general form of the project. Literally. Create a diagram explaining each of the main components of the project and how they fit together. Focus especially on processes that can be shared between components, so multiple members of the team aren't re-implementing the same things in different ways. This will also help you split up the workload in an equitable way. 12 | 13 | 2. If methods being developed by different members of the team include variables holding the same "things", decide on standardized names for these variables. The goal here is that if someone not in the project was to look at the code written by Bob and the code written by Alice, it would be immediately clear to them when Bob and Alice are manipulating the same object. 14 | 15 | 3. Decide on a consistent set of standards the whole team will follow. Things to consider include: 16 | - Function and variable naming: different casing should be used for public vs private methods. Global variables should be cased differently from local variables. I also like to use a standard form for temporary variables vs variables that will be used throughout a method. 17 | - Documentation: each function should have a doc-string style documentation. Decide both what information needs to be in the docstring and the formatting. 18 | 19 | 20 | # During the project 21 | 22 | Once you get started you should meet regularly so that everyone is on the same page regarding the state of the project. At these meetings, you should discuss challenges you're struggling with. Also, you will inevitably need to make changes to the structure of the project. You should discuss these changes, and update the "map" you made before starting so that it's always up to date. You should also do regular code review: each member of the team should review the code written by another member, not necessarily for quality assurance or correctness (though you should do this when methods are finished), but so that you know what the other members are doing and to make sure two people aren't implementing the same thing, that variables are consistently named, etc. Inevitably, you will realize you need to refactor something into a shared method. 23 | 24 | # General tips 25 | 26 | 1. Keep variable names consistent. If variable `user_name` is passed from function `main(...)` to `sum_hits(...)` to `output(...)`, the variable should be called `user_name` in all three functions. 27 | 28 | 2. Along the same lines, keep the order of variables in function signatures consistent. This one is easy, if you just always add new variables to the end of the function signature. -------------------------------------------------------------------------------- /how-to-craft-belonging.md: -------------------------------------------------------------------------------- 1 | - We are wired to connect 2 | - Belong is loosely "the feeling that your community respects, values, and cares for you" 3 | - The best predictor of retention for 4 year college students is whether they feel like they belong- AKA_ " I feel like there is a place for me here" 4 | - We are also highly attuned for threats of belonging, like microaggressions 5 | - The response to feeling not welcomed and when someone doesn't feel they belong is PAIN. In fact, the same centers in brain for physical pain are active when there is social pain and non-belonging 6 | - When hiring, people who are looking at job candidates will change the applicant rating criteria to for the applicants to rationalize in their head whether the applicant belongs or not. People who are hiring that say they are the most objective are usually the most biased in hiring. 7 | - One way to facilitate belonging is asking people about their values- What do they live for? What would they die for? 8 | - Transition spaces and times (like going into a lab meeting, welcoming a new member to the team, starting a new job, etc) are stressful and are times we feel like we do not belong. The people who are already in the spaces can faciltate belonging by welcoming the new person in their space. Even simple things like hello and introducing yourself help facillitate beloging. 9 | For leaders and senior folks, telling your mentees that "you belong and it is normal to feel unsure and that you don't belong here. Everyone goes through it" is very powerful and can help in retention. Share stories of when you felt you didn't belong. This is also key step to see other people who look like you (as they made it through the rough time and so can you). 10 | - For more, there is a book that Geoffrey wrote- https://wwnorton.com/books/9781324006183 11 | 12 | 13 | _This belonging files comes from notes taken by Ben Rush at the Teaching and Learning Symposium at UW-Madison on May 19th, 2023 during the plenary lecture given by Geoffrey Cohen_ -------------------------------------------------------------------------------- /interest-in-lab.md: -------------------------------------------------------------------------------- 1 | # Are you interested in joining the Solis-Lemus lab? 2 | 3 | - If you are an undergraduate student: 4 | - currently enrolled at UW-Madison looking for research experience, read [this section](#undergrad) 5 | - wanting to apply to grad school at UW-Madison, read [this section](#apply) 6 | - If you are a graduate student: 7 | - currently enrolled (or soon to start) at UW-Madison interested in joining the lab or doing a rotation, read [this section](#grad) 8 | - wanting to apply to grad school at UW-Madison, read [this section](#apply) 9 | - wanting to apply for a postdoc position, read [this section](#applypostdoc) 10 | - If you are a postdoc: 11 | - wanting to apply for a postdoc position in the lab, read [this section](#applypostdoc) 12 | - wanting to apply to your own funding with me as supervisor, read [this section](#postdocfunds) 13 | 14 | ## Are you an undergraduate student currently enrolled at UW-Madison looking for research experience? 15 | 16 | I receive many applications for research positions in my lab and can only accept students who are serious about the effort involved and where there is a good fit with my group. 17 | 18 | First of all, please read the rules regarding undergraduate research in the lab: 19 | - All research led by undergraduate students is expected to produce either a publication or software. For this reason, only highly motivated students looking for long-term research opportunities (at least one year in the lab) are welcome. 20 | - Short-term projects are sometimes available in the lab. If you are interested in one-semester or one-summer work, feel free to email me to let me know about this interest, but there is no guarantee that there will be a project that will accomodate to this timeline. 21 | - Seniors are not admitted to join the lab as there is not enough time to do meaningful research. The best time to join the lab is the beginning of junior year or the summer immediately before junior year. 22 | - Knowledge of version control via git/github is a must as well as interest on good computing practices, team work and science communication. 23 | - There will be a trial period in which you will be assigned to an existing project. This trial period will give you the opportunity to learn if the lab is a good fit for you. 24 | - Team work is highly valued in the lab, so you are expected to fully participate in meetings, symposia and other events 25 | 26 | Advantages of joining the lab: 27 | - Participate in state-of-the-art research as the leader of a project 28 | - Gain research experience that is valuable for graduate school and data science industry jobs (computing practices, reproducibility, science communication, research independence) 29 | - Plenty of opportunities to improve science communication (talks, posters, papers) 30 | - Co-authorship on publications produced in the lab with your contribution (read the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md)) 31 | - Network with other students in the lab and in WID 32 | - Strong commitment to mentoring by me and other senior students in the lab 33 | - Support with grad school/job applications as well as carefully written honest letters of recommendation highlighting your strengths in research 34 | 35 | ### Am I a good fit for the lab? 36 | 37 | 1. Take the [git quiz](https://www.w3schools.com/git/git_quiz.asp) 38 | - If you scored 8 or higher, you are in great shape! 39 | - If you scored less than 8, you need to study git/github. Study [these notes](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) carefully 40 | 41 | 2. Read the [best computing practices](https://github.com/crsl4/mindful-programming/blob/master/lecture.md#1-best-computing-practices) of the lab and answer the following questions: 42 | - Am I interested in producing code that is well-documented and commented? 43 | - Am I interested in spending a lot of time making sure my code is understandable to others and it follows good computing practices? 44 | - Am I interested in following the structure for file names and folders? 45 | - Am I interested in learning git/github using the terminal? 46 | 47 | 3. Read the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) and answer the following questions: 48 | - Am I interested in participating in lab meetings, WID meetings and student events? 49 | - Am I interested in presenting my research in symposia via talks or posters? 50 | - Am I committed to see the project through either by finishing up all steps during my time in the lab or by helping other students take over the project? 51 | 52 | ### Expected timeline when you join the lab 53 | 54 | Timeline varies depending on the nature of the project, but this example can serve to illustrate the different stages: 55 | - Summer before junior year (2-3 months): learn about your project and necessary background knowledge, learn good computing practices and git/github through the terminal, trial period on existing project 56 | - Fall/Spring junior year (2 semesters): work on your project as independent research or as part of a team of students 57 | - Summer before senior year: usually students do internships, so no work in the lab, but students could be involved in short-term projects if they choose to or continue working on their projects 58 | - Fall senior year (1 semester): write paper for publication or deploy software. Deadline of December 1 so that the new product (paper/software) can be included in grad school or job application 59 | 60 | ### After reading this document, I am still interested in joining the lab! 61 | 62 | Great! Follow the next steps: 63 | 64 | 1. Fill out [this google form](https://forms.gle/8B8c1hcMUr5tXZeW7) which is the collaboration agreement 65 | 2. Email me your CV and transcript with the subject "Data Science Undergrad Research". Write down in the email that you have read this document and filled out the collaboration agreement form. Include in the email meeting times that would work for you for the following two weeks. 66 | 67 | After you send the email, we will schedule a meeting to chat. Expect to answer questions about yourself (major, year, research interests) as well as about programming skills and knowledge of git and computing practices. It will not be an exam, but I will be curious to know your experience. During this meeting, I will also highlight existing projects in the lab to assess if they would be interesting to you. 68 | 69 | 70 | ## Do you want to apply to graduate school at UW-Madison in my lab? 71 | 72 | Research is highly multi-disciplinary! So, I welcome graduate students interested in different programs: 73 | 74 | - **PhD in Plant Pathology: Application deadline December 1** (email me regarding Spring admission). Application info [here](https://plantpath.wisc.edu/application-process/). 75 | - **PhD in Statistics: Application deadline December 1** (no admissions in Spring). Application info [here](https://stat.wisc.edu/graduate-studies/phd-program/) 76 | - **PhD in Mathematics: Application deadline December 15** (no admissions in Spring). Application info [here](https://www.math.wisc.edu/node/11) 77 | - **PhD in Biomedical Data Science: Application deadline December 15** (no admissions in Spring). Application info [here](https://biostat.wiscweb.wisc.edu/education/prospective-students/) 78 | 79 | Even though my research is purely computational (dry lab), I am happy to co-advise students interested in empirical research, together with [another professor in the department](https://plantpath.wisc.edu/faculty-3/). 80 | 81 | Note that admission to the programs is done by committees, not by individual faculty (so, not by me), but I would be happy to help you in the application process. 82 | 83 | If you are a biology-oriented student, you need to have an interest in computational biology or bioinformatics to join the lab. Students doing a bio-oriented PhD can complement their training in statistics and data science with: 84 | - [MS in Statistics](https://stat.wisc.edu/graduate-studies/ms-program/) 85 | - MS in Applied Stat (upcoming Fall 2022) 86 | - [MS in Biometry](https://stat.wisc.edu/graduate-studies/biometry/) 87 | - [Minor in Quantitative Biology](https://qbi.wisc.edu/) 88 | 89 | Next steps for you: 90 | - Read more about the [lab research](https://solislemuslab.github.io//pages/research.html) and identify projects that interest you 91 | - Watch this [YouTube video](https://www.youtube.com/watch?v=z3nbG6MUJvM) on details on how to join the lab and the lab culture 92 | - Read the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) 93 | - Feel free to email me if you are interested in working with me and have questions regarding the application 94 | - Make sure to include your CV and unofficial transcript in the email as well as details on what specific projects attract you from the lab 95 | - If you have read the lab guidelines, make sure to comment on this too in your email 96 | 97 | ## Are you a graduate student currently enrolled at UW-Madison interested in joining the lab (or doing a rotation)? 98 | 99 | - Master/PhD students are welcome to join the lab or to do a rotation 100 | - I can serve as PhD advisor of students in the following programs: 101 | - Statistics 102 | - Mathematics 103 | - Plant Pathology 104 | - Biomedical Data Science 105 | - Research in the lab is highly interdisciplinary, so students from different fields are welcome as all projects can be tailored to mathematical or statistical theory, computational implementations, machine learning, or biological applications 106 | - Advantages of joining the lab: 107 | - Participate in state-of-the-art research as the leader of a project 108 | - Gain research experience that is valuable for postdoc positions and data science industry jobs (computing practices, reproducibility, science communication, research independence) 109 | - Plenty of opportunities to improve science communication (talks, posters, papers) 110 | - Co-authorship on publications produced in the lab with your contribution (read the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md)) 111 | - Network with other students in the lab and in WID 112 | - Strong commitment to mentoring by me and other senior students in the lab 113 | - Support with grad school/job applications as well as carefully written honest letters of recommendation highlighting your strengths in research 114 | - All PhD students start with a short trial period (rotation) where both parties (me and you) will decide if you are a good fit for the lab and the lab is a good fit for you. For stat or math students, it is a good idea to explore different advisor options. 115 | 116 | Questions to ask yourself before deciding to join the lab: 117 | - Do I like research on mathematics, statistics, data science, machine learning, software development or biological applications? 118 | - For bio-oriented students, do I have an interest in computational biology/bioinformatics to produce methods and software? 119 | - Have I read the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) and do I agree with them? 120 | - Have I read about the [research in the lab](https://solislemuslab.github.io//pages/research.html) and identified some areas that interest me? 121 | - Logistic questions 122 | - Do I need RA funding necessarily or do I have support from my department as TAships? 123 | - If you are a PhD student: do I want to do a short rotation in the lab first before deciding? 124 | 125 | Next steps: 126 | - Send me an email with your CV and unofficial transcript as well as your interest in working with me and what type of projects interests you most (e.g. theoretical math/stat, computational, data analyses, software development). Include in the email meeting times that would work for you for the following two weeks. 127 | - After you send the email, we will schedule a meeting to chat. Expect to answer questions about yourself (undergrad degree, research experience, research interests) as well as about programming skills and knowledge of git and computing practices. During this meeting, I will also highlight existing projects in the lab to assess if they would be interesting to you. 128 | 129 | 130 | ## Do you want to apply for a postdoc position in the lab? 131 | 132 | I am interested in collaborating with postdocs with any research background: biology, computer science, statistics, mathematics from theoretical/computational work to empirical. 133 | 134 | For people with computational biology/statistics/data science background, there are several opportunities to become involved in ongoing projects related to my research: phylogenetic networks, bayesian phylogenetic inference, high-dimensional highly-correlated regression models applied to genomic/biological data, machine and deep learning, among others. 135 | In addition, I am also excited to work with people interested in empirical research by teaming up with other faculty in the department. 136 | 137 | In any scenario, I'd be happy to provide assistance in the application to fellowships and grants to support your own independent research agenda. 138 | 139 | 140 | Postdocs in the lab are expected to lead projects and grow as fully independent researchers, so in order to start a conversation, you need to: 141 | - Read the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) 142 | - Read the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md) 143 | - Read the [postdoc guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/postdoc-guidelines.md) 144 | - Be familiar with [research in the lab](https://solislemuslab.github.io//pages/research.html) and read several papers produced in the lab 145 | - Identify a project (or several projects) that you would like to work on and start pitching ideas in a rustic [project plan](https://github.com/solislemuslab/lab-dynamics/blob/master/project-plan.md) (goal, background, objectives). I am happy to fall outside of the lab's comfort zone if you have a good project plan! 146 | 147 | 148 | Send me an email (subject "Postdoc application") with: 149 | - CV 150 | - two names of recommenders 151 | - short paragraph describing your current research 152 | - links or PDFs of X publications you have co-authored, and explain the role you had in each publication (0 < X < 4) 153 | - a pitch of potential project plan (goal, background, objectives) that we could work on together 154 | - meeting times for the following two weeks 155 | 156 | 157 | ## Do you have your own independent research ideas as a postdoc and you want to apply to your own funding with me as a supervisor? 158 | 159 | First of all, great idea pursuing your own sources of funding! Not only gives you the flexibility to work on the project you love, but it also builds a stronger CV with evidence of external funding. 160 | 161 | I am happy to serve as your postdoc supervisor on any postdoc fellowship/awards/grants and even help you with the application. To find some options for postdoc funding (some do not require citizenship), see [here](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md#postdoc). 162 | 163 | Send me an email (subject "Postdoc application with own funding") with: 164 | - CV 165 | - short paragraph describing your current research 166 | - information on the fellowship/award/grant you want to submit as well as deadline 167 | - pitch of the project proposal you will submit (goal, background, objectives) 168 | - what do you need from me? Letter of support, feedback on the project proposal,... 169 | - meeting times for the following two weeks 170 | -------------------------------------------------------------------------------- /lab-guidelines.md: -------------------------------------------------------------------------------- 1 | # Code of Conduct 2 | 3 | From [The Carpentries CoC](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html): 4 | 5 | - Use welcoming and inclusive language 6 | - Be respectful of different viewpoints and experiences 7 | - Gracefully accept constructive criticism 8 | - Focus on what is best for the community 9 | - Show courtesy and respect towards other community members 10 | 11 | # Solis-Lemus lab guidelines 12 | Based on (shamelessly copied from) "Guidelines for Research in the Baum lab" by David Baum. 13 | _This is a dynamic document; feel free to suggest modifications to improve these general guidelines._ 14 | 15 | ## What I expect from you: 16 | - You will take ownership of your experience 17 | - **Acknowledge that you have the primary responsibility for the successful completion of your work.** You should maintain a high level of professionalism, self-motivation, engagement, scientific curiosity, and ethical standards. 18 | - **Ensure that you meet regularly with me** (once per week would be ideal) and provide me with updates on the progress and results of your activities and experiments. At the same time, be aware of my time constraints. I will strive to keep an open door policy, but there will be times when I won't be able to meet, and you will need to figure things out on your own. Acquiring problem-solving skills is part of a good research program. 19 | - **Be knowledgeable of the policies of the institute and university.** Comply with all institutional policies, including intellectual property rules, and codes of conduct. 20 | - For grad students with 33-50% RAships, this means enrolling in full time credits (at least 8 credits for non-disserators and 3 credits for dissertators) every semester. 21 | 22 | - You will be a team player 23 | - **Attend and actively participate in all laboratory meetings**, as well as relevant seminars. Participation in lab meetings does not mean only presenting your own work, but also providing support to others in the lab through constructive questions and shared insights. 24 | - Please provide _one-week_ notice if you will miss meetings due to classes or exams 25 | - Please report any travel _one month_ in advance. Use the google spreadsheet in slack. 26 | - **Strive to be the very best lab citizen.** Be respectful, tolerant of, and work collegially with all lab colleagues: respect individual differences in values, personalities, work styles, and theoretical perspectives. 27 | - **Acknowledge the efforts of everyone in the lab.** 28 | 29 | - You will develop strong research skills 30 | - **Take advantage of your opportunity to work at a world-class university by developing and refining stellar research skills.** I expect that you will already know or learn how to plan, design, and conduct high quality empirical, conceptual and/or theoretical research. More importantly, I expect that you are open to improve your skills (research/computational/writing) constantly 31 | - **Be responsive to advice and constructive criticism.** Remember that the feedback you get from me, your colleagues, your committee members, and your course instructors is intended to improve your scientific work. Do not take criticism personal and use it as an opportunity to grow as a scientist. 32 | - **Present your work at meetings/seminars and prepare scientific articles.** The ‘currency’ in science is published papers, they drive a lot of what we do and, because our lab is supported by taxpayer dollars, we have an obligation to complete and disseminate our findings. I will push you to publish your research. I expect that your manuscripts/presentations will adhere to the [Guidelines on manuscripts and code](#mscode). Please expect that at the beginning, I may heavily rewrite and edit your manuscripts 33 | - Note that everyone in the lab is expected to do one local presentation per year, and graduate students and postdocs (and optional for undergraduate students) should do one conference presentation per year 34 | - **You will follow the best computing practices in all the code/scripts that you do.** There is a big gap between code that runs, and code that is suitable for publication/open-source software (see [Guidelines on manuscripts and code](#mscode)). 35 | - **You will be reproducible.** Maintain detailed, organized, and accurate records of your research. Be aware that your notes, records and all tangible research data are my property as the lab director. When you leave the lab, I encourage you to take copies of your work with you. But one full set of all files/notes must stay in the lab, with appropriate and accessible documentation. 36 | - **Keep up with the literature** so that you can have a hand in guiding your own research. Block at least one hour per week to do lit searches and read articles. 37 | 38 | 39 | - You will work to meet deadlines 40 | - **Strive to meet deadlines**: this is the only way to manage your progress. Deadlines can be managed in a number of ways, but I expect you to work your best to maintain these goals. As long as you are meeting expectations, you can largely set your own schedule. 41 | - **Be mindful of the constraints on my time.** Allow a minimum of one week prior to submission deadlines for me to read and respond to short materials such conference abstracts and two weeks for me to work on manuscripts or grant proposals. Please do not assume I can read materials within a day or two, especially when I am traveling. 42 | 43 | - You will communicate clearly 44 | - **Let me know the style of communication or schedule of meetings that you prefer.** If there is something about my mentoring style that is proving difficult for you, please tell me so that I can have an opportunity to find an approach that works for you. 45 | - **Be prompt.** Respond promptly (in most cases, within 48 hours) to emails/slack messages from anyone in the lab group and show up on time and prepared for meetings. If you need time to gather information in response to an email/slack message, please acknowledge receipt of the message and indicate when you will be able to provide the requested information. 46 | - **Discuss policies on work hours, sick leave and vacation with me directly.** Consult with me and notify fellow lab members in advance of any planned absences. Post-docs and staff are expected to work at least 40 hours per week. Most lab members will not exceed two weeks per year of fully personal travel. I believe that work-life balance and vacation time are essential for creative thinking and good health and encourage you to take regular vacations. Be aware, however, that there will necessarily be times when it may not be ideal to schedule time away (e.g. first week of the semester for mandatory lab meeting to go over lab guidelines) 47 | - It is the lab member's responsibility to bring up any personal vacation or travel at least 2 weeks in advance and to reschedule any meetings 48 | - **Discuss policies on authorship and attendance at professional meetings with me** before beginning any projects to ensure that we are in agreement. I expect you to submit relevant research results in a timely manner. Barring unusual circumstances, it is my policy that researchers are first-author on all work for which they took the lead on the project and preparation of the initial version of the manuscript (but read the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md) for more information). 49 | - **Help other students with their projects and provide informal mentorship.** This is a valuable experience! If you want to add other individuals as authors to your papers, please discuss this with me early on and before discussing the situation with these potential co-authors. 50 | 51 | 52 | ## What you can expect from me: 53 | - **I will work tirelessly for the good of the lab group**; the success of every member of our group is my top priority. I will be transparent about the lab’s financial situation and honest about the amount of further funding that I can provide. 54 | - I will be available for regular meetings and informal conversations. At our scheduled one-on-one meetings (ideally every week or every two weeks), we will address questions or concerns that you have. If you need to miss a meeting, it is your responsibility to reschedule; I will show you the same courtesy. Slack is the best way to communicate with me. I do not always respond on weekends as I spent this time with my family. If my office door is open, feel free to stop by. 55 | - I will involve you in the process of writing grant proposals, from the original ideas through submission. The goal of this is to help expose you to this important aspect of science and help you contribute to my efforts to fund your work and the lab in general. 56 | - I will discuss authorship policies regarding papers with you. I will acknowledge your scientific contributions to the work in my laboratory, and I will work with you to help you publish your work in a timely manner (read the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md) for more information). 57 | - **You can count on me to do my very best to promote you as a scientist and your work**. I will help you in your professional development and in your efforts to communicate your work. I will work very hard to adequately fund our laboratory and to disseminate its results. I will do my best to provide timely review of your research. 58 | - My primary role is to (1) help you think clearly about theoretical issues driving your research and (2) successfully bring in grants and to steward our resources so that we all benefit to the maximum extent from our joint efforts. I will also make every attempt to help you network into the scientific community, including assistance finding post-doctoral and faculty positions. 59 | - I am committed to mentoring you, even after you leave my lab. I am committed to your education and training while you are in my lab, and to advising and guiding your career development – to the degree you wish — long after you leave. I will provide honest letters of evaluation for you when you request them. 60 | - **I am committed to your research projects.** I will help to plan and direct your projects, set reasonable and attainable goals, and establish a timeline for completion of projects. 61 | - I will not require you to perform tasks that are unrelated to your professional development. 62 | - I will lead by example and facilitate your training in complementary skills needed to be a successful scientist, such as oral and written communication skills, lab management, and scientific professionalism. I will encourage you to seek opportunities in teaching or outreach, provided these remain manageable in scope. 63 | - I will encourage you to attend scientific/professional meetings and will make an effort to fund such activities. I will not be able to cover all of requests but I will try. 64 | - I will provide you a work environment that is intellectually stimulating, emotionally supportive, safe, and free of harassment. I will intervene strenuously to ensure that everybody feels safe and welcome. 65 | - I will strive to be supportive, equitable, accessible, encouraging, and respectful. I will try my best to understand your unique situation. I am mindful that we all come from a different backgrounds and have different circumstance. It will help if you keep me informed about your experiences and remember that academic research is a job with very high expectations. I view my role as fostering your professional confidence and encouraging your critical thinking, skepticism, and creativity. **If my attempts to do this are not effective for you, I am open to talking with you about other ways to achieve these goals.** 66 | 67 | 68 | # Guidelines for manuscripts, presentations, and code 69 | 70 | ## Best computing practices for code 71 | 72 | - I expect that you will 73 | - read and adhere to the guidelines in [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) 74 | - study resources on computing practices, reproducibility, version control, organization of projects, naming files. There are some links in [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) that I expect that you will study, understand and follow when programming 75 | - understand that reproducibility is a process. No one is reproducible from one day to the next. It is a constant process, and it will feel unnatural a times 76 | - assume that everything that you are doing right now will need to be redone at some point in the future: be prepared 77 | - ask for help if you need it. **If you are feeling overwhelmed or stressed or don't know where to start, please reach out and I am happy to talk with you to find solutions** 78 | - note that if you are already reproducible and keep good notes by other means (not highlighted here), do continue that way! In fact, I am always eager to learn different ideas! **This document is not meant to force anyone to do one particular style of best computing and reproducibility practices.** Just keep in mind that whatever your style, we should discuss it and make sure that we are all on the same boat when it comes to expectations and outcomes 79 | 80 | ### Does my code (simulations/data analysis/software) satisfy the lab computing practices? Checklist 81 | - Is all my code on the github repo, properly documented and commented? 82 | - Does the repo have an explicit readme describing the usage, citation, format of the repo and feedback/issues section? 83 | - Does the repo have a license, contributing guidelines and documentation? 84 | - If it is a new software tool, does it have a wiki or website tutorial? 85 | 86 | ## Clear scientific communication: manuscripts and presentations 87 | 88 | It is not enough to do "good science", we need to be good communicators of our science. 89 | 90 | - I expect that you will 91 | - actively search ways to improve your oral and communication skills 92 | - accept that at the beginning I may heavily edit your manuscripts. Don't feel discouraged! It is part of the learning process that we accept feedback from peers. My manuscripts are still edited by colleagues and co-authors all the time! 93 | - be genuinely interested in communicating your science to any type of audience in a simple and effective manner 94 | - use the many university resources (like the Writing Center) to your advantage 95 | - accept that good skills in academic writing are a key component in a scientist's development 96 | - practice your presentations with multiple people, and be responsive to constructive criticism 97 | - make writing clear manuscript and delivering clear presentations a priority for your growth as a scientist 98 | - work hard on the first complete draft of the manuscript before you share it with me and co-authors. You do not want to share a document that is half-baked or not easy to read. You want to be respectful of your co-authors' time by putting your best work forward 99 | - check out the [resources](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md) such as [10 simple rules for concise scientific writing](https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lol2.10165) by Scott Hotaling 100 | - acknowledge that it is our job as communicators to connect with different audiences (statisticians, biologists, general public) and communicating our ideas effectively is not an "extra burden", it is at the core of our work as scientists 101 | 102 | ### Manuscripts 103 | - By the time that you finish your first complete version of the manuscript (to send to co-authors), I expect that your manuscript will 104 | - be properly structured (e.g. introduction, methods, simulations, data analysis). Look at options in the journal/conference of interest to follow specific guidelines related to manuscript structure 105 | - be well-written. We are constantly learning writing skills, so your manuscript is not expected to be perfect. But you should strive to make an effort to make it understandable and use all necessary resources at your disposal 106 | - contain good quality figures to present results, but perhaps not in perfect form yet 107 | - be in the conference/journal format if we have already decided where to submit. This is important in case there are page limits that we need to consider when revising the manuscript 108 | - have the proper citations 109 | 110 | - By the time the manuscript is ready for submission, I expect that your manuscript will 111 | - be fully reproducible, everything must be backed up and supported by data, simulations, scripts 112 | - be accompanied by a github repo with the necessary reproducible scripts, textfiles, notes, ... to reproduce the analysis and simulations 113 | - be well-written, and that you have incorporated the feedback/suggestions from the co-authors 114 | - have high-quality figures 115 | - have a graphical abstract, if suitable 116 | 117 | #### Is my manuscript ready for submission to journal? Checklist 118 | - Does it include an extensive literature search (cite everybody)? 119 | - Does it include a graphical abstract and/or summary box for easy reading? 120 | - Are the figures of high quality (good choice of colors: color-blindness aware)? 121 | - Are simulations and data analysis fully reproducible, easy to follow by others and pushed to a github repo? 122 | - Is it well-written and following the rules of concise scientific writing? 123 | - Is it submitted to arxiv or biorxiv? 124 | 125 | #### My paper is published, now what? 126 | In recent years, it has becoming increasingly important to advertise broadly our work and invest heavily on good science communication strategies. We will 127 | - create a 3-min lighting talk to post on the [lab youtube channel](https://www.youtube.com/channel/UCcBcmxIYYGC6Z04p9SC7hwg/featured) 128 | - this presentation should include: 1) motivation, 2) our solution to the problem, 3) some results, 4) advertisement of the paper and github, 5) acknowledgements. Check out [this previous talk](https://www.youtube.com/watch?v=IXLVDIKxPvk) as an example 129 | - tweet the paper alongside 130 | - an image of the graphical abstract or an infographics (see [canva](https://www.canva.com/tools/infographic-maker-v1/)) or a [word cloud](https://www.wordclouds.com/) 131 | - a link to the youtube 3-min presentation 132 | - post in the [lab instagram](https://www.instagram.com/thestatistician/?hl=en) a wordcloud and a 1-min presentation of the paper 133 | - include the paper in the lab website (alongside links to the lightning talk and images of the graphical abstract/infographic/word cloud) 134 | - email the paper to collaborators 135 | - do presentations in conferences and symposia ([more info](#talks)) 136 | - if the published paper is for a software tool, create a video tutorial and a wiki documentation 137 | - add a folder in `/mnt/dv/wid/projects4/SolisLemus-shared-data` in the lab server with the real data that you used (raw and clean) along with a readme file describing the steps from raw to clean 138 | 139 | ### Talks/posters in conferences and symposia 140 | 141 | All abstracts, posters, and talks that you work on in the lab are representations of the lab and must be approved by me before submission. 142 | 143 | #### Is my talk/poster ready for presenting? Checklist 144 | - Have you presented in lab meeting to get feedback from others? 145 | - Have you shared your slides/poster with me or others in the lab to check for errors/typos? 146 | - Have you timed yourself to make sure you adhere to the presentation guidelines? 147 | - Have you included an Acknowledgement slide at the end to acknowledge the lab, other collaborators and sources of funding (you can use [the template](https://docs.google.com/presentation/d/1E4vFh4RDh-xHzRRSe1krvt6vrzzBZHQs4jQMrxOzWgQ/edit?usp=sharing))? 148 | - Do you include QR codes or links to your paper/software? 149 | - Are you giving proper citation to others' work in your slides/poster? 150 | 151 | #### Travel logistics for conferences 152 | 153 | Please discuss with me any plans of conferences to make sure that we have the necessary funding. 154 | 155 | Steps for conference attendance: 156 | 1. Write the abstract and send to me for approval before submitting it. Please give the abstract to me at least 2 weeks prior to the abstract submission deadline 157 | 2. Upon receipt, please forward the acceptance email to the conference to me 158 | 3. You can register to the conference on your end and get reimbursed, or if it is too expensive, we can cover the cost directly at WID. 159 | 4. Do not book flights or make hotel reservations before reading the [travel rules](https://widkipedia.wid.wisc.edu/travel-reimbursement/)! You should always email Janine Harrison and Becky Streich to help with the travel plans. 160 | 161 | 162 | 163 | -------------------------------------------------------------------------------- /lit-review.md: -------------------------------------------------------------------------------- 1 | # Learning phylogenetic networks 2 | 3 | 0. Introduction to phylogenetics 4 | - [Evolution 101](https://threadreaderapp.com/thread/1477332222206423041.html) 5 | - Phylogenetics 101 youtube videos by Paul Lewis [Part 1](https://www.youtube.com/watch?v=1r4z0YJq580). Other parts 2,3,4 are also good to check out 6 | - [Phylogenomics book](https://hal.inria.fr/PGE/page/table-of-contents) 7 | 8 | 1. Understanding probabilities of gene trees under a species tree with the coalescent model: [Degnan2005](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2005.tb00891.x) 9 | 10 | 2. Understanding probabilities of gene trees under a species network with the coalescent model: 11 | - [Yu2012](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002660) 12 | - [Yu2014](https://www.pnas.org/content/111/46/16448) 13 | 14 | 3. Understanding maximum likelihood estimation on species networks and traversals of network space: [Yu2014](https://www.pnas.org/content/111/46/16448) 15 | 16 | 4. Understanding maximum pseudolikelihood estimation on species networks to improve scalability: [SolisLemus2016](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896) 17 | 18 | 5. Understanding bayesian inference on species networks: 19 | - [Wen2016](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006006) 20 | - [Zhang2017](https://academic.oup.com/mbe/article/35/2/504/4705834) 21 | 22 | 6. Understanding identifiability of networks: 23 | - from pseudolikelihood perspective: [SolisLemus2016](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896), [SolisLemus2020](https://arxiv.org/abs/2010.01758) 24 | - from likelihood perspective: [Zhu2017](https://academic.oup.com/sysbio/article/66/2/283/2682287) 25 | - from displayed trees (not coalescent-based): [Pardi2015](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004135) 26 | 27 | 7. Review papers on phylogenetic networks: 28 | - [Degnan2018](https://academic.oup.com/sysbio/article/67/5/786/5017269) 29 | - [Blair2019](https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz056/5552158) 30 | - [Kong2021](https://arxiv.org/abs/2109.10251) 31 | - [Elworth2019](https://link.springer.com/chapter/10.1007/978-3-030-10837-3_13) 32 | 33 | 8. Moves in network space: [Gambette2017](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005611) 34 | 35 | 8. Understanding the julia package PhyloNetworks: 36 | - [Tutorial](https://github.com/crsl4/PhyloNetworks.jl/wiki) 37 | - [SolisLemus2017](https://academic.oup.com/mbe/article/34/12/3292/4103410?guestAccessKey=1d2c94f2-f064-42ae-a652-ce14cd095442) 38 | 39 | 9. Network simulators 40 | - [Zombi (python)](https://academic.oup.com/bioinformatics/article/36/4/1286/5578480) 41 | - [ipcoal (python)](https://www.biorxiv.org/content/10.1101/2020.01.15.908236v1) 42 | - [HybridSim (java)](https://academic.oup.com/gbe/article/8/5/1299/2939560). [Github](https://github.com/MichaelWoodhams/HybridSim) 43 | - [NetGen (C)](https://academic.oup.com/bioinformatics/article/22/15/1921/242472) 44 | - [Birth-Hybridization (BEAST2)](https://academic.oup.com/mbe/article/35/2/504/4705834) 45 | - [SiPhyNetwork](https://github.com/jjustison/SiPhyNetwork) 46 | 47 | 48 | # Deep learning in biology 49 | 50 | - [Ten quick tips for deep learning in biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009803) 51 | - [Avoiding common pitfalls in machine learning omic data science](https://www.nature.com/articles/s41563-018-0241-z) 52 | - [Navigating the pitfalls of applying machine learning in genomics](https://www.nature.com/articles/s41576-021-00434-9) 53 | - [Deep learning as a tool for ecology and evolution](https://ecoevorxiv.org/nt3as/) 54 | - [Current progress and open challenges for applying deep learning across the biosciences](https://www.nature.com/articles/s41467-022-29268-7) 55 | 56 | # Phylogenetics in languages 57 | 58 | - [Notes by Johann Mattis-List](https://hcommons.org/deposits/item/hc:50621/) -------------------------------------------------------------------------------- /lor-guidelines.md: -------------------------------------------------------------------------------- 1 | # Guidelines to request letter of recommendation 2 | 3 | In order for me yo write you a letter of recommendation for graduate school, please read this document carefully and follow the steps. 4 | 5 | ## 1. Make sure to start with plenty of time 6 | I will need to know the programs you will be applying to, as well as relevant information about your application at least three weeks before the first deadline. It is a good idea to start working on your application with time. You usually want to have a full draft of the application and list of programs by early October. 7 | 8 | ## 2. To request LOR, first collect the following information 9 | - For every program: 10 | - University 11 | - Name of the program 12 | - Deadline 13 | - Program link 14 | - Physical address of the department/school 15 | - CV 16 | - Personal statement (it does not need to be the final polished version, but a good complete draft) 17 | 18 | ## 3. Fill out a google form per program 19 | Three weeks before the first deadline (or November 15 whatever happens first), you need to 20 | - fill out [the google form](https://forms.gle/ozvDqMxaPhvXdh399) for each of the programs in your list. That is, if you need letter of recommendation for 15 programs, you need to fill out the google form 15 times with the information of each program. Since I work on the letters in bulk, I need to know of all programs roughly at the same time. For example, if you are applying to 15 programs and the first deadline is November 15, you need to fill out the google form with all 15 programs by October 25. LORs to programs not in the original list can be approved under extenuating circumstances. 21 | - send me by email or slack your CV and draft of personal statement 22 | 23 | **VERY IMPORTANT (read this carefully):** 24 | - A script will extract the information that you type in the google form, so be extra careful with typoes and the way you want your name to appear in the letters; also, **avoid all symbols like parenthesis, commas, &, #**. 25 | - Example: you should write the complete name of the university with the first letter capitalized. If you only write "cornell", this is how it will appear in your letter of recommendation and it won't look professional. 26 | - Note that here is no limit to the number of letters that you can ask me as long as you follow the rules described and I am also happy to give you feedback on your application if you want. 27 | - If you are lumping the letters of a given university (when you are applying to multiple programs within the same department/school), feel free to only fill out the form once and write down: "X,Y,Z" in the "name of program". 28 | - When filling out the information on the application, select that I am your "research advisor" when describing our relationship. 29 | - We need to have been working for at least 6 months together for me to be able to write a letter of recommendation for you. 30 | 31 | -------------------------------------------------------------------------------- /on-off-boarding.md: -------------------------------------------------------------------------------- 1 | # Onboarding steps 2 | 3 | 1. Read the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) and the [computing and reproducibility practices](https://github.com/crsl4/mindful-programming/blob/master/lecture.md). For the computing practices, you can start by watching this [YouTube video](https://youtu.be/7KCqpL0cde8) 4 | 2. Fill out the [lab info form](https://forms.gle/E9tuHPuvWc4cHaNa6) 5 | 3. If you are an undergraduate student, fill out [this collaboration agreement](https://forms.gle/8B8c1hcMUr5tXZeW7) 6 | 4. Do you feel confident with git? Fill out this [self-assessment quiz](https://forms.gle/3VR7PRtEkiGtCJoFA). If it is too hard, check out some resources [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) 7 | 5. Add yourself to the [lab website](https://solislemuslab.github.io//pages/people.html) via a pull request. Please choose a photo that is not too high resolution so that the file is not too heavy for github. 8 | 6. Read and sign the [authorship guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/authorship.md) 9 | 7. If you are a grad student or postdoc, start thinking about your [project plan](https://github.com/solislemuslab/lab-dynamics/blob/master/project-plan.md) 10 | 11 | 12 | 13 | # Offboarding steps 14 | 15 | We are sad to see you go, but excited for the new posibilities in your future! 16 | 17 | Steps before you leave the lab: 18 | 19 | 1. Make sure to document all your work and leave an updated version of any incomplete project in github. If you have files in the cluster, make sure to clean them up and back up anything that you need to take with you 20 | 2. Remove yourself from the [lab website](https://solislemuslab.github.io//pages/people.html) (repo [here](https://github.com/solislemuslab/solislemuslab.github.io)) (do not remove your photo from the files though as it will be used when presenting your work in the future) and add yourself to the "Past members" section. Please include where you will be (if you already know) and include a link to your website. You will do this via a pull request. You should be familiar with github by now, but if you are not sure how to do this, check some github resources [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) 21 | 3. Email Pat Pointer and Em Craft from WID to let them know that you will leave my lab so that she update your WID account (either remove it or change it to other lab). Please copy me in this email 22 | 4. Email `alumni@wid.wisc.edu` with the information of the program you graduated from (e.g. Master in Statistics) and year (or if you are a postdoc, simply say that you were a postdoc) and the information on where you will be now to appear in the WID alumni newsletter 23 | 4. Fill out the offboarding form with your new contact information [here](https://forms.gle/Utj4pTHwMe456zyMA). This is so that I can reach out regarding our projects together (publications, extensions to our work, presentations,...) 24 | 25 | Note that you will keep access to your project slack workspace, but not to the lab slack workspace which will be reserved for current lab members only. 26 | -------------------------------------------------------------------------------- /postdoc-guidelines.md: -------------------------------------------------------------------------------- 1 | --- 2 | geometry: margin=1.5cm 3 | output: 4 | pdf_document: default 5 | html_document: default 6 | --- 7 | # Postdoc guidelines in the Solis-Lemus lab 8 | 9 | ### What to expect when you join the lab: 10 | - We will have a conversation early on about your future career plans to devise a strategy together 11 | - Claudia will be fully committed to your growth and success as a scientist and to help you reach your career goals 12 | - We will have a clear conversation about projects that belong to the lab and independent projects that will belong to you after you leave 13 | - Claudia will provide you with constant opportunities to grow on important academic skills: 14 | - academic writing 15 | - science communication skills 16 | - peer reviewing for journals 17 | - good computing practices 18 | - mentoring skills 19 | - conference presentations 20 | - grant writing skills 21 | - Claudia will fully support your quest to find your own fellowships or funding 22 | - Aside from your academic success, your emotional, physical and spiritual well-being will always be a priority in the lab 23 | 24 | 25 | ### What is expected of you: 26 | - You will read and follow the lab guidelines: see [here](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) 27 | - You will follow the best computing practices (highlighted [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md)) on 28 | - folder organization 29 | - file names 30 | - version control with git/Github 31 | - reproducibility 32 | - clear and well-commented code 33 | - You will write the project plan (see format [here](https://github.com/solislemuslab/lab-dynamics/blob/master/project-plan.md)) for the project that we agree to work on together (described in a separate document) within ___ weeks of your arrival to the lab 34 | - The project plan should be the first item to agree on as it will guide the whole project 35 | - We can discuss and revise this document together prior to the final version we will agree on 36 | - You will have the intellectual freedom to propose how the project(s) should be tackled and your strategy will be reflected in the project plan that we will both agree on 37 | - You will be the leading force of the project(s) that we agree to work on together (described in a separate document) 38 | - You are expected to be first author in the paper(s) and Claudia will be last/corresponding author (see authorship guidelines) 39 | - You will have the opportunity to mentor graduate or undergraduate students to work with you on this project 40 | - Aside from the main project(s) that we agreed to work on together (described in a separate document), you are welcome to work on other side projects as long as you distribute time: 80% on the lab projects and 20% on the side projects 41 | - All side projects should be discussed with Claudia so that she knows the different projects you are working on at a given time (e.g. to avoid adding extra tasks on your plate) 42 | 43 | ### Other rules: 44 | - The Solis-Lemus lab deeply values good science communication: writing, quality of figures and paper presentation needs to be approved by Claudia to make sure that they satisfy the requirements of good science communication 45 | - The Solis-Lemus lab deeply values open-source software so methodological papers should be accompanied by open-source software hosted on Github and whenever possible, published as software that others can use 46 | - All abstracts, posters, talks, preprints and papers that you work on in the lab are representations of the lab and must be approved by Claudia before submission 47 | 48 | 49 | Name of postdoc: 50 | 51 | Signature of postdoc: 52 | 53 | Date: -------------------------------------------------------------------------------- /project-plan.md: -------------------------------------------------------------------------------- 1 | # Writing a project plan 2 | Based on the "Cooking recipe" for writing a project plan by Doerte Doepfer. 3 | 4 | This document is mostly for graduate students and postdocs. But if you are an undergraduate student that wants to do a project plan, please talk to me! 5 | _This is a dynamic document; please suggest modifications to improve these general guidelines._ 6 | 7 | ## 11 steps towards writing the project plan 8 | 9 | 1. Identify the main goal of the project and capture it in a title 10 | 2. Develop the background of the research problem in 2 to 5 sentences ending with a ‘gap’ of knowledge that you will address. What would you describe about this topic to someone who is not familiar with it? 11 | 3. Develop the overall objective: in 1-2 sentences, describe what is the main goal of the project 12 | 4. State the specific aims: the specific goals of the proposed research. This is like a recipe of the steps that you will do to accomplish the overal objective, usually 3-4 specific aims along with a short description 13 | 5. State the significance: why does this matter? why should the world care about this research? (2-5 sentences) 14 | 6. State the innovation: what is new about your project compared to existing approaches? (2-4 sentences) 15 | 7. List of deliverables: these are actual products that will come out of this project. Examples: publication(s), open source software to distribute, conference presentation(s), grant proposal(s). Provide details to which journals/conferences/grant mechanisms you want to submit (with deadlines if possible) 16 | 8. Timeline for your deliverables: how long do yo expect to work on each aim (roughly)? You can be as descriptive and detailed as you want, or simply provide rough estimates. This plan is for you to help you to guide your research to completion. Make sure to include deadlines in the timeline (if you have any, for example, for conferences) 17 | 9. People in the team: do you need other people to succeed in this plan? If you are a graduate student, do you think that having undergraduate students helping you on some parts of the project would be beneficial and how? If you are a postdoc, do you think that having graduate students or undergraduate students working with you could be beneficial? Sometimes having extra students on the project is not possible, so you perhaps do not want to state that you necessarily need X students working with you for the success of the project, but you can highlight potential work that could be delegated 18 | 10. Potential limitations and alternatives: What are the main barriers that you expect to encounter? What is your plan to overcome those barriers? What would happen if the research you propose does not work out? What are your alternatives? Can you try other approaches? 19 | 11. Future work: If the research proposed is successful, what else could be done afterwards with this theory? What are natural extensions to this work? 20 | 21 | ## Final stages 22 | 1. Read and re-read and re-read your proposal. Try to visualize it from someone else's perspective 23 | 2. Use the resources of the [Writing Center](https://writing.wisc.edu/)! They have one-on-one help to polish written work 24 | 3. Show your project plan to many people to get feedback. It is good if you share your project plan with people outside your area of expertise 25 | 4. Discuss the project plan with the PI 26 | 5. Understand that the project plan is a mutable object that will be constantly evolving as you work on the project 27 | 28 | ## Things to keep in mind regarding the deliverables 29 | - The deliverables must be up to standards with the [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md) of reproducibility, clear communication, etc. You do not need to think about these guidelines as you prepare the project plan, but they are important to know as you write your timeline. That is, do not expect that you will send your manuscript to co-authors and it will be submitted for publication within one week 30 | 31 | - The most common deliverable will be manuscripts. Keep in mind that you will be the first author of this manuscript, so make sure to consider this in the timeline. That is, the first author is responsible for: 32 | - Writing the manuscript 33 | - Revising the manuscript and corresponding with the journal or publisher;] 34 | - Designing the project plan (often in collaboration with other members of the research team) 35 | - Obtaining approval of all coauthors on the final draft, and 36 | - Understanding the general principles of **all the work** included in the manuscript. 37 | 38 | - Another common deliverable will be open-source software. Keep in mind that there is a huge gap between code that runs, and code that is suitable for publication and you should consider this in your timeline. Follow reproducibility practices and best computing practices (examples in [lab guidelines](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md)). Keep in mind that suboptimal code will not be deemed suitable for publication -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- 1 | # Solis-Lemus lab 2 | 3 | - I am potentially interested in joining the lab -> read [this document](https://github.com/solislemuslab/lab-dynamics/blob/master/interest-in-lab.md) 4 | - I am joining the lab -> read the [onboarding steps](https://github.com/solislemuslab/lab-dynamics/blob/master/on-off-boarding.md) 5 | - I am leaving the lab -> read the [offboarding steps](https://github.com/solislemuslab/lab-dynamics/blob/master/on-off-boarding.md) 6 | - I want to request a letter of recommendation -> read [this document](https://github.com/solislemuslab/lab-dynamics/blob/master/lor-guidelines.md) 7 | - I have to create a project plan -> read [this document](https://github.com/solislemuslab/lab-dynamics/blob/master/project-plan.md) 8 | - I think my project is ready to be submitted to a journal -> read [this](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md#manuscripts) 9 | - I want to attend a conference to present my work -> read [this](https://github.com/solislemuslab/lab-dynamics/blob/master/lab-guidelines.md#talks) -------------------------------------------------------------------------------- /resources.md: -------------------------------------------------------------------------------- 1 | There are many skills that we need to informally learn in academia: written and oral communication skills; reproducibility; lab dynamics like working on a team, giving/accepting constructive feedback; getting your own funding... Here I've compiled a list of resources (hopefully up to date) to learn more about some of those skills. 2 | 3 | # Reproducibility and best computing practices 4 | 5 | - [Steps for reproducible research YouTube talk](https://www.youtube.com/watch?app=desktop&v=rNQ-RlG3JnQ&feature=youtu.be) by Karl Broman (highly encouraged!) 6 | - Motivating reading on the importance of reproducibility: [Nature collection](https://www.nature.com/news/reproducibility-1.17552) 7 | - The importance of Open Science in Andrew Gelman's [blog](https://statmodeling.stat.columbia.edu/2020/06/11/bla-bla-bla-peer-review-bla-bla-bla/) 8 | - My notes on [mindful programming](https://github.com/crsl4/mindful-programming/blob/master/lecture.md) 9 | - [Tools for Reproducible Research](http://kbroman.org/Tools4RR/) by Karl Broman 10 | - [Reproducible programming for biologists who code](https://ben-heil.github.io/2020-06-16-mustdo/) by Ben Heil 11 | - [Data organization in spreadsheets](https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375989) by Karl Broman and Kara Woo 12 | - JSM 2020 [Panel on version control with git in stat cources](https://github.com/mdbeckman/JSM2020-Virtual) 13 | - [Intro to Computational thinking in Julia](https://computationalthinking.mit.edu/Spring21/) MIT class by Alan Edelman, David P. Sanders & Charles E. Leiserson 14 | - [Reproducible and Trustworthy Workflows for Data Science](https://ubc-dsci.github.io/reproducible-and-trustworthy-workflows-for-data-science/README.html) by Tiffany A. Timbers, Joel Ostblom, Florencia D’Andrea, Rodolfo Lourenzutti 15 | 16 | ## Learning to code? 17 | 18 | There are many free resources online to learn how to code for people of all ages and background (thanks to Cecile Ane for pointing at some of these resources!): 19 | 20 | - [Scratch](https://scratch.mit.edu/): free coding community 21 | - [Raspberry Pi](https://www.raspberrypi.org/) 22 | - [Microbit](https://microbit.org/) 23 | - Not learning resource, but coding environment: [CodePen](https://codepen.io/) 24 | - Learn to code with [CodeAcademy](https://www.codecademy.com/) 25 | - Bootcamps or code clubs: 26 | - [Resilient Coders Bootcamp](http://resilientcoders.org/bootcamp) 27 | - [BlackGirlsCode events](https://www.blackgirlscode.com/events/) 28 | - [Basics of C++](https://hsf-training.github.io/hsf-training-cpp-webpage/) 29 | 30 | - Learning Julia? 31 | - Some links in my lab website [here](https://solislemuslab.github.io//pages/teaching.html) 32 | - [YouTube intro talk](https://www.youtube.com/watch?v=8h8rQyEpiZA) 33 | - [Numerical Linear Algebra](https://nhigham.com/2022/10/11/seven-sins-of-numerical-linear-algebra/) by Nick Higham 34 | - [The Big six matrix factorizations](https://nhigham.com/2022/05/18/the-big-six-matrix-factorizations/) by Nick Higham 35 | 36 | # Peer-reviews and publishing (Sci comm) 37 | 38 | - [JEFworks guide to peer review](https://jef.works/blog/2020/03/23/a-guide-to-scientific-peer-review/) 39 | - [Connected papers](https://www.connectedpapers.com/) is a visualization tool to see how papers in a certain field are connected. This is helpful when finding papers or experts related to a topic 40 | - Some thoughts on [authorship guidelines](https://github.com/SeedscapeEcology/Policies/blob/master/Authorship_Guidelines.md) from the [Beckman Research Group](http://seedscape.github.io/BeckmanLab/) 41 | - Improve scientific writing: [10 simple rules](https://aslopubs.onlinelibrary.wiley.com/doi/full/10.1002/lol2.10165) by Scott Hotaling 42 | - Improve tables with R: [Guidelines for better tables](https://themockup.blog/posts/2020-09-04-10-table-rules-in-r/#rule-1-offset-the-heads-from-the-body) by Thomas Mock 43 | - [Elevator pitch](https://graduateschool.nd.edu/assets/76988/elevator_pitch_8_28_2012.pdf): how to present your research by Gretchen Busl 44 | - [Good figures](https://www.biostat.wisc.edu/~kbroman/presentations/graphs_MDPhD2014.pdf) by Karl Broman 45 | - [Ten rules for better figures](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833) by Rougier et al 46 | - [Ten rules to colorize](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008259) by Hattab et al 47 | - [Publishing papers while keeping everything in balance](https://ojs.library.queensu.ca/index.php/IEE/article/view/9045) by Scott Hotaling 48 | - [BioRender](https://biorender.com/) for professional figures 49 | - [Unsplash](https://unsplash.com/) for high resolution photos 50 | - [The noun project](https://thenounproject.com/) for icons and photos 51 | - [Writing rejections](https://cloudistro.com/5-reasons-you-should-aim-for-100-literary-rejection-letters-in-2021/). Blog on why to set a goal to get 100 literary rejection letters this year (written for writers but applies to all). 52 | - [ggplot2 guide](https://evamaerey.github.io/ggplot2_grammar_guide/about) by Gina Reynolds and [the evolution of ggplot2](https://www.cedricscherer.com/2019/05/17/the-evolution-of-a-ggplot-ep.-1/) by Cedric Scherer 53 | - [Seeds of Science](https://www.theseedsofscience.org/) journal. 54 | - [Bioinformatics and publication figures](https://jlsteenwyk.com/resources.html) by Jacob Steenwyk. 55 | 56 | # Getting funding 57 | 58 | Showing that you are able to acquire your own funding is very important in the academic landscape. Even if you are fully funded by your department or PI, consider applying to a scholarship or fellowship to learn valuable grant writing skills and improving your CV. 59 | A few examples below. 60 | 61 | - [Advice on grant writing](https://threadreaderapp.com/thread/1478838265763418112.html) by Betty Lai 62 | 63 | ## Undergraduate and Graduate 64 | 65 | - List of scholarships and fellowships that do not require US citizenship in [ImmigrantsRising](https://immigrantsrising.org/2020scholarships/) 66 | 67 | - NSF Graduate Research Fellowship [GRFP](https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=6201) 68 | 69 | ## NSF GRFP 70 | 71 | - [Examples in evolutionary biology](https://github.com/ybrandvain/GRFP) by Yaniv Brandvain 72 | - [Advice](https://clairemckaybowen.com/fellowship/) by Claire McKay Bowen 73 | - [Advice](http://www.malloryladd.com/nsf-grfp-advice.html) by Mallory P. Ladd 74 | - [Advice](https://www.alexhunterlang.com/nsf-fellowship) by Alex Lang 75 | 76 | ## Postdoc 77 | 78 | - NIH K99/R00 Path to Independence [award](https://researchtraining.nih.gov/programs/career-development/k99-r00) (for postdocs; no need of US-citizenship) 79 | - [NIH grant writing samples](https://www.uab.edu/ccts/research-commons/grant-help/proposal-development/grant-library?utm_source=home&utm_medium=banner&utm_campaign=sixpack&utm_content=) 80 | 81 | - Burroughs Wellcome Fund Career Awards at the Scientific Interface [CASI](https://www.bwfund.org/grant-programs/interfaces-science/career-awards-scientific-interface) (for postdocs; no need of US-citizenship) 82 | 83 | - [Branco Weiss Fellowship](https://brancoweissfellowship.org/) (for postdocs; no need of US-citizenship) 84 | 85 | - [Marie Curie Individual Fellowships](https://ec.europa.eu/research/mariecurieactions/actions/individual-fellowships_en) (for postdocs; no need of US-citizenship) 86 | 87 | - [List of postdoc fellowships](https://docs.google.com/spreadsheets/u/1/d/1J2M_tQgoqV4ivpfEClh9qs9f2KQN2O1G3Jpda2aoHfQ/htmlview) 88 | 89 | 90 | ## Within UW-Madison 91 | - Graduate School funding [options](https://grad.wisc.edu/funding/) 92 | - Computation and Informatics in Biology and Medicine [CIBM traineeships](http://www.cibm.wisc.edu/) 93 | - Quantitative Biology Initiative (QBI): info [here](https://qbi.wisc.edu/) and [training grants](https://qbi.wisc.edu/education/training-grants/) 94 | 95 | 96 | # Lab dynamics 97 | 98 | - Assertiveness in [NIH training handout](https://www.training.nih.gov/assets/Assertiveness_Handout.pdf) 99 | - Thanks for the feedback [TedTalk youtube](https://www.youtube.com/watch?v=FQNbaKkYk_Q) by Sheila Heen 100 | - NIH Workplace dynamics [series](training.nih.gov/leadership_training) 101 | - Virtual NIH [activities](https://www.training.nih.gov/virtual_nih_activities_for_trainees_outside_the_nih) 102 | - 4 bad habits in managers in [Ideas TED](https://ideas.ted.com/do-you-have-any-of-these-4-bad-habits-of-managers-heres-how-to-change-them/amp/?__twitter_impression=true) 103 | - [EMBO lab leadership workshops](https://lab-management.embo.org/course-overview) 104 | - [Ultimate guide to productivity](https://blog.doist.com/personal-productivity-methods/) 105 | - [Colautti lab standards](https://colauttilab.github.io/Manifesto/index.html#Colautti_Lab_Standards) 106 | - [Lindsey lab expectations](https://lindseylab.files.wordpress.com/2020/06/lindsey_lab_expectations_20200616.pdf) 107 | - [Fancy publication figures](https://github.com/alperezq/FancyPubFigures) 108 | - [Untools](https://untools.co/) for productivity, communication and problem solving 109 | - [12ft ladder](https://12ft.io/) for paywalls 110 | - [PhD voices](https://phdvoice.org/free-resources/) 111 | - [Academic secret menu](https://docs.google.com/document/d/1Cl_u8Qq4DD6ROKH4SNThxyLF7UWTWuWKEaVhrKCJqOw/edit?usp=sharing) 112 | - [Meeting planner](https://www.timeanddate.com/worldclock/meeting.html) 113 | 114 | # Statistics 115 | 116 | - The history of statistics: Github [repo](https://github.com/sctyner/history_of_statistics) by Sam Tyner 117 | - [Statistical Rethinking in Julia](https://github.com/StatisticalRethinkingJulia/StatisticalRethinking.jl) by Richard McElreath 118 | - [Statistical Rethinking in R](https://bookdown.org/content/4857/) by A Solomon Kurz 119 | - [Statistical Rethinking in Julia](https://shmuma.github.io/rethinking-2ed-julia/) 120 | - [Statistical Rethinking](https://github.com/rmcelreath/stat_rethinking_2023) course materials by Richard McElreath 121 | - [YouTube lectures](https://www.youtube.com/watch?v=cclUd_HoRlo) 122 | - [Modern Statistics for Biology](https://www.huber.embl.de/msmb/introduction.html) by Susan Holmes and Wolfgang Huber 123 | - [Calling Bullsh*t](https://callingbullshit.org/index.html): Data reasoning in a digital world by Carl Bergstrom and Jevin West 124 | - [The role of p-values](https://www.tandfonline.com/doi/full/10.1080/19466315.2020.1724560) by Eric Gibson 125 | - [Ten quick tips for effective dimensionality reduction](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006907) by Lan H. Nguyen and Susan Holmes 126 | - [Seeing Theory](https://seeing-theory.brown.edu/index.html#firstPage): A visual introduction to probability and statistics by Daniel Kunin, Jingru Guo, Tyler Dae Devlin, and Daniel Xiang 127 | - [Graphs+Networks workshop materials](https://sites.tufts.edu/vrdi/gn-materials/) and [reading list](https://sites.tufts.edu/vrdi/gn-readings/) by MGGG Lab Outreach 128 | - [IMS World symposium 2020](https://www.worldsymposium2020.org/program/prerecorded-talks) pre-recorded talks 129 | - [Seminar Math Data Science 2020](https://sites.google.com/view/seminarmathdatascience/home) pre-recorded talks 130 | - [SVM Dual formulation](https://medium.com/@sathvikchiramana/svm-dual-formulation-7535caa84f17) post by Sathvik Chiramana 131 | - [Learning stat with R](https://ourcodingclub.github.io/tutorials.html) 132 | - [Learning optimization algorithms](https://www.youtube.com/playlist?list=PLXsmhnDvpjORzPelSDs0LSDrfJcqyLlZc) 133 | - [Summer Institutes: SISMID 2021](https://si.biostat.washington.edu/suminst/sismid2021/modules) 134 | - [Data Analysis in R](https://bookdown.org/steve_midway/DAR/) by Steve Midway 135 | - [StatQuest](https://www.youtube.com/channel/UCtYLUTtgS3k1Fg4y5tAhLbw) YouTube channel by Josh Starmer 136 | - [Julia for Data Science](https://www.juliafordatascience.com/) by Josh Day and [book](https://juliadatascience.io/) by Storopoli, Huijzer and Alonso 137 | - [What they forgot to teach you about R](https://rstats.wtf/) by Jennifer Bryan 138 | - [Neural networks intro](https://cs231n.github.io/convolutional-networks/) 139 | - [Stats Camp](https://www.statscamp.org/) 140 | - [Data Organization](https://kbroman.org/dataorg/) by Karl Broman 141 | - [Bayesian data analysis course](https://avehtari.github.io/BDA_course_Aalto/gsu2021.html) by Aki Vehtari 142 | - [CSV community conference for data makers everywhere](https://csvconf.com/speakers/) 143 | - [Bayesian Learning Course](https://github.com/mattiasvillani/BayesLearnCourse) by Mattias Vilani 144 | - [Blog about SVD decomposition](https://www.govindgnair.com/post/svd-is-almost-all-you-need/) 145 | - [Bayesian statistics in R](https://oliviergimenez.github.io/bayesian-stats-with-R/) by Olivier Gimenez 146 | - [Democratizing Artificial Intelligence Research, Education, and Technologies](https://dair.ai/) 147 | - [Bayesian Optimization book](https://bayesoptbook.com/) by Roman Garnett 148 | - [Machine learning for biologists](https://carpentries-incubator.github.io/ml4bio-workshop/) by the Gitter lab 149 | - [Matrix calculus](http://www.matrixcalculus.org/) 150 | - [Hack your data beautiful](https://psyteachr.github.io/hack-your-data/) 151 | 152 | # Diversity and inclusion in science 153 | 154 | - [Black Girls Code](https://www.blackgirlscode.com/donations.html) 155 | - [Resilient Coders](http://resilientcoders.org/) 156 | - [SACNAS](https://www.sacnas.org/who-we-are/): Society for the Advancement of Chicanos/Hispanics and Native Americans in Science 157 | - [ABRCMS](https://www.abrcms.org/): Annual Biomedical Research Conference for Minority Students 158 | - Diversity and Inclusion Lab [Posters](https://sammykatta.com/diversity) 159 | - Academics for Black Survival and Wellness [website](https://www.academics4blacklives.com/) 160 | - [Bias Watch Neuro](https://biaswatchneuro.com/about/) 161 | - [Whiteness in hiring committees](https://www.hepgjournals.org/doi/pdf/10.17763/1943-5045-87.4.557) 162 | - [Grace Hopper Celebration conference](https://ghc.anitab.org/about/our-history/) 163 | - [Rising Stars](https://eecs.berkeley.edu/rising-stars-2020): an academic career workshop for women in EECS 164 | - [Project BioDiversify](https://projectbiodiversify.wpcomstaging.com/sex/): Tools for promoting diversity and inclusivity in biology classrooms 165 | - [The Underrepresentation Curriculum Project](https://underrep.com/): A flexible curriculum designed to help students critically examine scientific fields and take action for equity, inclusion and justice 166 | - [Latino Youth Summit](https://precollege.wisc.edu/latino-youth-summit/) at UW-Madison 167 | - [Gender equality in academia report](https://research.pasteur.fr/wp-content/uploads/2021/04/research_pasteur-jobim-2021-pilotproject-genderspeakingdifferencesin-academia-gender-equal-and-.pdf) Junhanlu ZHANG, Rachel TORCHET & Hanna JULIENNE and accompanying [paper](https://www.biorxiv.org/content/10.1101/2022.03.07.483337v2) 168 | 169 | 170 | ## Within UW-Madison 171 | - [WISELI](https://wiseli.wisc.edu/workshops/) Women in Science and Engineering Leadership Institute 172 | - [WID Anti-Racist Resources](https://wid.wisc.edu/category/anti-racist-resources/) 173 | - [SciMed](https://scimedgrs.wisc.edu/) 174 | 175 | # Teaching and learning 176 | - Using GitHub classroom and Travis CI [blog](https://github.blog/2019-02-12-how-github-classroom-and-travis-ci-improved-students-grades/) 177 | - [The Super Mario Effect](https://www.youtube.com/watch?v=9vJRopau0g0): Tricking your brain into learning more by Mark Rober TEDxPenn 178 | 179 | # Microbiome 180 | - Statistical methods in Microbiome Research [workshop notes](https://web.stanford.edu/class/bios221/Pune/) by Susan Holmes and Leo Lahti 181 | - [STAMPS2019](https://github.com/mblstamps/stamps2019/wiki) 182 | - [History of metagenomics](http://merenlab.org/2020/07/27/history-of-metagenomics/) by Matthew Schechter 183 | - [Microbial Omics for beginners](https://www.youtube.com/playlist?list=PL7133RHfhW-MwCLz-c2DZxAmtoHipqBcL) by the Meren Lab 184 | - [Omics vocabulary](https://anvio.org/vocabulary/) by Eren lab. 185 | 186 | # Networking 187 | - [Tutorial for github website](https://kbroman.org/simple_site/) by Karl Broman 188 | - [Academic github website](https://github.com/academicpages/academicpages.github.io) 189 | 190 | # Mastodon 191 | - What is Mastodon? https://tilvids.com/w/hRzMpJwSkqEK3ZTNPbSuqu 192 | - [Guide to Mastodon: fedi tipes](https://fedi.tips/) 193 | - Find Twitter people in Mastodon: https://fedifinder.glitch.me/ 194 | - [Open Science community](https://germanrepro.github.io/Mastodon-OpenScience/) 195 | - [Guide to Mastodon](https://github.com/joyeusenoelle/GuideToMastodon) 196 | - [The 5-minute guide to the fediverse and Mastodon](https://gist.github.com/joepie91/f924e846c24ec7ed82d6d554a7e7c9a8) 197 | - [Everything I know about Mastodon by Danielle Navarro](https://blog.djnavarro.net/posts/2022-11-03_what-i-know-about-mastodon/#what-is-mastodon-what-is-the-fediverse) -------------------------------------------------------------------------------- /things2know.md: -------------------------------------------------------------------------------- 1 | # Things I wished I knew as an undergraduate student 2 | - Having a good folder and file organization is crucial for peace of mind. Take the time to organize your files so that everything is logical and easy to find (at least to you) 3 | - Take classes on academic writing, science communication, giving talks and doing poster presentations 4 | - Become proficient on git/github through the terminal. Some resources [here](https://github.com/crsl4/mindful-programming/blob/master/lecture.md). 5 | - Learn to use the terminal and to use a job scheduler for big computing needs. See [software carpentry](https://uw-madison-datascience.github.io/2019-06-13-uwmadison-swc/) for example. 6 | - Learn about reproducibility in science. Some resources for reproducibility [here](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md#reproducibility-and-best-computing-practices). 7 | 8 | # Things I wished I knew as a graduate student 9 | - Taking good notes of everything you do is incredibly important! All simulations, data analysis and even short code for sanity checks should be well-explained with readme/textfiles and scripts. It feels like a waste of time at the moment to take notes, but you save much time and energy in the long run when you need to redo things (which will always happen) 10 | - Having a good folder and file organization is crucial for peace of mind. Take the time to organize your files so that everything is logical and easy to find (at least to you) 11 | - Rejection is inevitable in academia and it is rarely a reflection of you. Do your best, but don't feel discouraged when your work is not appreciated by others. Use the opportunity to learn better ways to get your point across and connect with your audience (reviewers) 12 | - Good science communication skills are just as important as the science itself. Some resources on science communication [here](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md#peer-reviews-and-publishing-sci-comm) 13 | - Do not compare yourself to others! We all have our own strengths and weaknesses. Just focus on you! 14 | 15 | # Things I wished I knew as a postdoc 16 | - It is crucial to have in your CV that you are able to get funding, some resources [here](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md#getting-funding). 17 | - It is not enough to give talks, you need to give talks that are easy to understand by the audience. Always think about your audience! Some resources on science communication [here](https://github.com/solislemuslab/lab-dynamics/blob/master/resources.md#peer-reviews-and-publishing-sci-comm). 18 | - You need your research products to follow some story. You do not want your work to be "de chile, manteca y dulce" as we say in Mexico (all over the place). There has to be some central theme and it should be clear that you are working to become an expert in a niche. It is easier to convince recruiters that you are becoming an expert in a given area when all your work is backing up that narrative. --------------------------------------------------------------------------------