Useful links Author: Yingxiao Yan # longitools https://longitools.bsc.es/vre/home/ # 0. the best links AI related documents https://drive.google.com/drive/folders/1DaNlqYfzJN9uk6CzM6uL6C6cHI47WpIg Microsoft copilot https://copilot.microsoft.com/ CV writing https://www.cv.se/ ## information retrival https://www.perplexity.ai/ ## production https://chatgpt.com/ Use chatGPT4all locally https://github.com/nomic-ai/gpt4all https://codeornocode.com/tutorial/how-to-run-chatgpt-local-gpt4all/#:~:text=How%20to%20run%20a%20ChatGPT%20model%20locally%20and,Document%20collection%20setup%206%206.%20You%E2%80%99re%20all%20set%21 The thing is I need to get nerlify token to and all the password Generate promt in chat GPT, and use that prompt in preplexity. This is because perplexity has short memories. So the promt should be good. ## the literature citing links litmaps - search connetions between literatrues https://www.litmaps.com/ researchrabbit - the links between literatures https://researchrabbitapp.com/home Explainpaper -explain certain terminologies in the paper https://www.explainpaper.com/ Chatpdf - ask questions about the pdf text - NOT free https://www.chatpdf.com/ Scispace - very convenient in separate results, methods, limitations ... https://typeset.io/ elicit - NOT free https://elicit.com/notebook/1274365b-0abb-4728-8d91-546635ce9d1f connected papers https://www.connectedpapers.com/ ## Writing a literature review Writing a Literature Review 1. Structure. Ask perplexity.ai to suggest a structure. 2. Seed points. Use Elicit to suggest seed papers for each section in the structure. 3. Expand literature. Use ConnectedPapers or Research Rabbit (Find docs in pdf-format using Sci-hub) 4. Summarize papers. Use docAnalyzer.AI or some free alternative (see below) Here are some of the top free AI tools for summarizing scientific papers: **Scholarcy** is a free online tool that can summarize research papers and articles by extracting the key points and conclusions. It uses natural language processing to analyze the text and generate a concise summary. **ChatGPT,** the powerful language model from OpenAI, can summarize research papers when given the text or a link to the paper. Simply ask it to summarize the key findings and conclusions of the paper. **Resoomer** is a free online tool that specializes in generating argumentative summaries from research papers and articles. It aims to capture the main arguments, evidence, and reasoning in a condensed form. **Humata AI** is another free web-based tool that can summarize research papers by extracting the key points, findings, and conclusions. It supports summarizing PDFs and web articles. **SummarizeBot** is a free AI tool that summarizes research papers, articles, and documents by identifying the main concepts and critical passages using natural language processing. It offers customizable summary lengths and supports multiple languages. While these free tools can provide helpful summaries, their accuracy may vary across different subjects and paper complexity. For more advanced summarization capabilities, paid tools like Tenorshare AI - PDF Tool, Jasper AI, and SciSummary offer specialized features tailored for research papers. Some other free tools (or strong entry/free options for paid apps) **Heuristi.ca** AI-driven mindmap **OpenRead** Summaries **ExplainPaper** Summaries **PaperBrain** Summaries **Einblick.ai** Chart generation **Tavily.com** Research assistant **Powerdrill** RAG **Scispace** Summaries -> Copilot **Nextnet** Biomedicine and Life Sciences ## other materails for stuff https://bit.ly/snM_AI_material consensus AI GPT https://consensus.app/search/ deepl translator https://www.deepl.com/translator How to use AI in research https://docs.google.com/document/d/1e8FFFUQoiOfNIJ5UdCA0Z6_Qno1LOCEcmvqnEETMka4/edit ## Harness AI Day 1: https://youtu.be/M4bTibLrJY0 Day 2: https://youtu.be/zlSpG2iyj_s ## python https://docs.python.org/3/py-modindex.html python module index # 1.journal-related ## check which journal can be paid by chalmers library https://app.scifree.se/App#/PublicJournalSeeker/157!3006193 # 2.grant related ## Ask for digital signature https://edusign.sunet.se/sign/ ## A grant ask by gael https://kvvs.se/stipendier-och-anslag/ ## check for grants application https://intranet.chalmers.se/en/tools-support/research-utilisation/funding-of-research-innovation/find-research-calls/ ### link for chalmers foundation grant (the research fund) https://web103.reachmee.com/ext/I007/907/main?site=6&validator=6047c4abdf36af989c0490b8747f518e&lang=SE?rmpage=job&rmjob=315&rmlang=SE ### Grant shared by John https://hkjacobssonstiftelsen.se/ansokan/ ### link for internalization grant (PhD student) https://intranet.chalmers.se/en/tools-support/doctoral-studies-support/regulation-and-administration/admission-and-financing/ ### link for Adlerbert Foreign Student Hospitality Foundation (non-Swedish ppl) https://www.chalmers.se/en/education/study-at-chalmers/student-life/scholarships-for-enrolled-students/adlerbert-foreign-student-hospitality-foundation/ ### Erasmus (for stuff inclusing phd students) https://intranet.chalmers.se/en/working-at-chalmers/employee/professional-career-development/international-staff-mobility/ # 3. course/learning related ## Tools for reproductive research https://nbisweden.github.io/workshop-reproducible-research/home_schedule.html ## Nordic RSE research software engineering https://nordic-rse.org/ ## Code refinary workshop https://coderefinery.org/lessons/ https://github.com/coderefinery/workshop-outro?tab=readme-ov-file https://coderefinery.github.io/installation/ https://www.twitch.tv/coderefinery https://coderefinery.org/ https://coderefinery.github.io/2024-03-12-workshop/#schedule https://coderefinery.github.io/git-collaborative/ https://coderefinery.github.io/reproducible-research/organizing-projects/ https://github.com/coderefinery/workshop-outro?tab=readme-ov-file questions and answers https://coderefinery.github.io/2024-03-12-workshop/questions/ ## snakemake https://snakemake.readthedocs.io/en/stable/ ## Scilifelab course webpage https://www.scilifelab.se/events/list/?tribe_eventcategory%5B0%5D=7655 ## Luke's blog fo coding page https://coding-club.rostools.org/ https://github.com/rostools/coding-club ## Luke's R course https://r-cubed-intermediate.rostools.org/ https://github.com/rostools/r-cubed-intermediate ## R conference and events https://www.r-consortium.org/news/events ## stuff week search http://staffmobility.eu/staff-week-search ## Latex https://www.overleaf.com/learn/latex/Learn_LaTeX_in_30_minutes#Creating_lists_in_LaTe Table generator in Latex https://www.tablesgenerator.com/ ### convert pdf to image https://smallpdf.com/pdf-to-jpg#r=result&t=6adcbdf7c8a326a81f06b15ebc210bfd&i=convert-to-image https://www.ilovepdf.com/download/yvgc5j7x9nv65f9h8dAcnt6zc0jdtwtvjphwjmnvgbs24j3yy8mcrrsspdq2lgf2zgcA3sppk6xvwfwlfn3zxc2dqxh9s51xknl8lk8sbqg1ytxnhlhApq6q8ldrb8m87c8070pmwytAh5w174cy3zy67kbkvdjhvkrmlrswy80hf20wxsgq/12 # 4.login page ## Naiss supr login https://supr.naiss.se/ recovery code 1457 5989 ## bianca login https://bianca.uppmax.uu.se/main/agent ## link for checking bianca status: https://status.uppmax.uu.se/ ## Very good bianca instructions/introductions https://uppmax.github.io/bianca_workshop/overview/ https://uppmax.github.io/bianca_workshop/intermediate/intro/ ## slurm intro https://www.uppmax.uu.se/digitalAssets/560/c_560271-l_1-k_uppmax-slurm-2022.pdf ## git, nextflow, snakemake, container, docker https://uppsala.instructure.com/courses/96483/modules https://github.com/NBISweden/workshop-reproducible-research.git CI/CD https://learn.gitlab.com/ci-consideration-mgr3/getting-started-gitlab-cicd?utm_medium=cpc&utm_source=bing&utm_campaign=singleappci_emea_pr_sitelink_nb_exact&utm_content=webcast-getting-started-gitlab-cicd_digital_x-pr_english_&&utm_term=cicd%20pipeline&_bt=&_bk=cicd%20pipeline&_bm=e&_bn=o&_bg=1324913161633099&msclkid=93222feb8e5611e1206f4a3e6f77af7e https://www.techtarget.com/searchsoftwarequality/CI-CD-pipelines-explained-Everything-you-need-to-know ## Metabocomp MetaboComp/MUVR (github.com) For MetaboComp the user name is chalmerscompmetabolomics@gmail.com and the password is Pro1337Haxx0r Sometimes you need to access gmail account. The user name is Gmail ChalmersCompMetabolomics@gmail.com and the password is Pro1337Haxx0r ## Publicly available training material: ENCCS develops and maintains a library of training material on topics in HPC, AI and Quantum Computing which is suitable for self-paced learning. Find the library at https://enccs.se/lessons/. ## Training events from around Europe Many HPC centres and National Competence Centres around Europe offer diverse HPC training workshops open to anyone in Europe, many of which are online. Upcoming workshops can be found at https://hpc-portal.eu/upcoming-events-courses. ## Introduction to python https://uppmax.github.io/uppmax_intro_python/sessions/using_the_python_interpreter/ https://docs.uppmax.uu.se/ module load python/3.11.4 # 5. some good technical explanations ## "xpply" functions (apply, sapply, lapply,vapply) https://ademos.people.uic.edu/Chapter4.html ## Introduction for data management practice https://uppsala.instructure.com/courses/52280/modules ## New quarto stuff https://quarto.org/docs/blog/posts/2024-10-15-conf-workshops-materials/ introduction https://posit-conf-2024.github.io/quarto-intro/ https://github.com/posit-conf-2024/quarto-intro https://posit-conf-2024.github.io/quarto-intro/materials/1-single-docs/1-welcome-to-quarto/slides.html https://posit-conf-2024.github.io/quarto-intro/materials/1-single-docs/2-polishing-docs/ Figures and tables, cross reference, callout, elements layout dashboard https://posit-conf-2024.github.io/quarto-dashboards/ https://github.com/posit-conf-2024/quarto-dashboards/tree/main website https://posit-conf-2024.github.io/quarto-websites/ https://github.com/cwickham/quarto-workshop-website ## quarto demo https://nbisweden.github.io/raukr-2023/labs/demo/ https://qmd4sci.njtierney.com/math Write formula in quarto ## Quarto lightbox Zoom in pictures https://github.com/quarto-ext/lightbox/ ## quarto extension ![image](https://hackmd.io/_uploads/BkLJQ2muC.png) Font Awesome https://github.com/quarto-ext/fontawesome QR Code https://github.com/jmbuhr/quarto-qrcode ## quarto slide root file https://quarto.org/docs/presentations/revealjs/ publish on gitlab https://www.youtube.com/watch?v=Sa13U9RHpIE quarto slide examples 1. source code: https://github.com/quarto-dev/quarto-web/blob/main/docs/presentations/revealjs/demo/index.qmd output: https://quarto.org/docs/presentations/revealjs/demo/#/title-slide 2. source code https://github.com/JauntyJJS/useR-2024 output: https://jauntyjjs.github.io/useR-2024/#/title-slide 3. main page https://rstudio-conf-2022.github.io/get-started-quarto/ Tutorial https://rstudio-conf-2022.github.io/get-started-quarto/materials/05-presentations.html#/your-turn-1 4. code: https://github.com/ClaudiuPapasteri/quarto-slide?tab=readme-ov-file output: https://claudiupapasteri.github.io/quarto-slide/quarto-slide.html#/11 5. code: output: https://gesiscss.github.io/quarto-workshop/material/slides/05_presentations.html#/title-slide 6. code and output https://tech.popdata.org/pma-data-hub/posts/2022-07-01-ined-revealjs/ ## rauk R material (very helpful) https://nbisweden.github.io/raukr-2023/contents.html ## unix command line tutorial https://swcarpentry.github.io/shell-novice/index.html ## Data integration of omics data https://payamemami.com/teaching/ ## about DAGs https://cbdrh.shinyapps.io/daggle/#using ## create personal website The website of quarto, which can be used as a template of own website https://github.com/quarto-dev/quarto-web/blob/main/_quarto.yml https://quarto.org/ https://www.emilyzabor.com/tutorials/rmarkdown_websites_tutorial.html#Personal_websites https://quarto.org/docs/websites/ https://www.marvinschmitt.com/blog/website-tutorial-quarto/#publishing-your-website-to-the-internet https://samanthacsik.github.io/talks_workshops/2022-08-05-creating-your-personal-website-using-quarto/ https://ucsb-meds.github.io/creating-quarto-websites/ https://www.wrprates.com/posts/website-with-quarto-automated-deployment/ https://gitlab.com/rwiederstein/quarto_example https://github.com/acbass49/personal_quarto_site/tree/main ## CV template for quarto https://github.com/mps9506/quarto-cv/ http://archive.schochastics.net/post/create-a-cv-with-quarto/ https://pkg.mitchelloharawild.com/vitae/ https://www.youtube.com/watch?v=cMlRAiQUdD8 https://github.com/tallguyjenks/CV/tree/master https://pkg.mitchelloharawild.com/vitae/ ## css and HTML https://www.w3schools.com/css/default.asp https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss ## scss https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss https://getbootstrap.com/docs/5.1/customize/css-variables/#root-variables ## fonts https://fonts.google.com/ https://developer.mozilla.org/en-US/docs/Web/CSS/font-family ## fontawesome(logo) https://fontawesome.com/download https://github.com/quarto-ext/fontawesome ## color codes https://www.rapidtables.com/web/color/RGB_Color.html ## color paletteer https://r-graph-gallery.com/ggplot2-color.html ## Python https://openbookproject.net/thinkcs/python/english3e/index.html https://uppsala.instructure.com/courses/85913/modules https://uppmax.github.io/uppmax_intro_python/afternoon_session/variables_expressions_and_statements_2/ ## app tutorial example https://isglobal-brge.github.io/exposome_bookdown/analysis-flowcharts.html#exposome-omic-integration-e.g.-crossomics ## Wrtie inline equations in normal R and in shiny https://www.haowulab.org/computing/Rtips/plotmath.html https://www.r-exercises.com/2017/10/21/mathematical-expressions-in-r-plots-tutorial/ https://sas-and-r.blogspot.com/2015/12/write-in-line-equations-in-your-shiny.html https://gallery.shinyapps.io/019-mathjax/ ## table1 https://www.rdocumentation.org/packages/table1/versions/1.4.3/topics/table1 https://cran.r-project.org/web/packages/table1/vignettes/table1-examples.html ## imputation If you use a vairbale in the analysis model, you should include them in the imputation model https://hanneoberman.github.io/presentations/2024/useR/slides.html#/title-slide slide https://stefvanbuuren.name/fimd/ missing data book https://hanneoberman.github.io/ personal website https://amices.org/ggmice/ ggmice https://hanneoberman.github.io/quickmice/ quick mice some funcitons for visualization visdat::vis_dat() naniar::vismiss() VIM::aggr() md.pattern() plot_pattern() ## mediation analysis https://codex.nimahejazi.org/steno2024_mediation_workshop/ https://netcoupler.github.io/NetCoupler/articles/NetCoupler.html ## github actions Integrate with quarto!!! https://quarto.org/docs/publishing/github-pages.html https://www.youtube.com/watch?v=arzBRW5XIkg An example https://github.com/steno-aarhus/mediation-analysis-course/blob/main/.github/workflows/build-netlify-website.yml Another exampl https://github.com/pbjarterot/Met-ID/blob/main/.github/workflows/main.yml some tutorial https://r-leyshon.github.io/blogging/blogs/03-quarto-github-actions.html ## linux https://hpc2n.github.io/intro-linux/ https://github.com/hpc2n/intro-linux https://umeauniversity.sharepoint.com/:w:/s/HPC2N630/Ed16r0fqgGpLm6T2u-bl5yIBZjmV_GvBy-EOsg9fcWK-UQ https://umeauniversity.sharepoint.com/:w:/s/HPC2N630/EQUtySAkcGREswBAeZiGJgUBilEListST0Oftyf2FqSnSg https://www.youtube.com/user/HPC2N https://www.hpc2n.umu.se/events/courses/2024/fall/intro-linux # 6. R books and materials ## Basic R https://r4ds.had.co.nz/index.html https://style.tidyverse.org/index.html ## advanced R https://adv-r.hadley.nz/index.html https://advanced-r-solutions.rbind.io/ ## R packages https://r-pkgs.org/ Write example for R script https://r-pkgs.org/man.html#sec-man-examples R code for https://r-pkgs.org/r-cmd-check.html#r-code ## HTTP testing in R https://books.ropensci.org/http-testing/index.html ## the high dimentional data in R https://dicook.github.io/mulgar_book/ ## tidyverse https://dplyr.tidyverse.org/reference/index.html https://style.tidyverse.org/pipes.html ## tidymodels https://www.tidymodels.org/ ## ggplot https://r-graphics.org/ learn ggplot with shiny app https://www.researchgate.net/publication/316145672_Learn_ggplot2_Using_Shiny_App ## visualization book https://clauswilke.com/dataviz/ ## shiny book https://mastering-shiny.org/index. ## shiny structures and tags https://rstudio.github.io/shinydashboard/structure.html#structure-overview https://shiny.posit.co/r/articles/build/tag-glossary/ https://rstudio.github.io/shinydashboard/structure.html#boxes ## shiny posit tutotial https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/ ## shiny nbis tutorial https://nbisweden.github.io/workshop-data-visualization-r/2304-canvas/lab_shiny1.html https://nbisweden.github.io/workshop-data-visualization-r/2304-canvas/lab_shiny2.html ## shinyapps.io use https://docs.posit.co/shinyapps.io/index.html ## How to write dependency for R description files https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html ## unit test https://contributions.bioconductor.org/tests.html ![image](https://hackmd.io/_uploads/r16jzkDB0.png) https://github.com/microbiome/mia/blob/devel/CONTRIBUTING.md ## structual equation modelling https://gabriellajg.github.io/EPSY-579-R-Cookbook-for-SEM/lavaan-lab-5-one-factor-cfa-model.html https://personality-project.org/r/tutorials/summerschool.14/rosseel_sem_cat.pdf https://nils-holmberg.github.io/sfac-r/web/sem/ https://www.azandisresearch.com/2024/07/24/structural-equation-modeling-in-r/ # 7. R repostories that is interesting ## progress https://github.com/r-lib/progress ## MetaboCombiner https://bioconductor.org/packages/release/bioc/vignettes/metabCombiner/inst/doc/metabCombiner_vignette.html https://github.com/bioc/metabCombiner?tab=readme-ov-file # 8. youtube links about stuff ## rarefying https://www.youtube.com/watch?v=g5BdGP4V5YA # 9. some knowledge specific link ICD code: diseases https://icd.who.int/browse10/2019/en#/K50-K52 ATC code: drug use https://www.whocc.no/atc_ddd_index/ # 10. Some repository's of Famous people ## Anton Ribbenstedt https://gitlab.com/parasitetwin/worklistmaker https://gitlab.com/parasitetwin/autoannotshiny https://github.com/MetaboComp/QualiMon ## Yingxiao Yan TriplotGUI: for visualization https://gitlab.com/YingxiaoYan/triplotgui StatTools: Tools for data manipulation/Statistics, (anything you can think of) https://gitlab.com/YingxiaoYan/StatTools ## Carl Brunius MUVR 1 https://gitlab.com/CarlBrunius/MUVR MUVR 2 https://gitlab.com/CarlBrunius/MUVR/-/tree/MUVR2?ref_type=heads ## Nuria https://github.com/nestanyol/CoolBeans ## Luke https://github.com/lwjohnst86?tab=repositories https://gitlab.com/lwjohnst ## some github page to learn from https://github.com/CogDisResLab/KRSA/tree/main/R https://github.com/pcastellanoescuder/pcastellanoescuder.github.io profile website from luke https://github.com/lwjohnst86/site https://lukewjohnston.com/ CV website from luke https://cv.lukewjohnston.com/ https://github.com/lwjohnst86/cv slide website and example slide from luke https://gitlab.com/lwjohnst/slides https://slides.lwjohnst.com/ https://slides.lwjohnst.com/s/2024-05-23/#/title-slide https://lukewjohnston.com/ https://github.com/lwjohnst86/site https://cv.lukewjohnston.com/ https://github.com/lwjohnst86/cv https://slides.lwjohnst.com/ https://gitlab.com/lwjohnst/slides https://posters.lwjohnst.com/ https://gitlab.com/lwjohnst/posters # Rights ## SULF calender https://sulf.se/en/calendar/