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 to run a ChatGPT model locally and,Document collection setup 6 6. You’re all set!

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[0]=7655

Luke's blog fo coding page

https://coding-club.rostools.org/

Luke's R course

https://r-cubed-intermediate.rostools.org/

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 pipeline&_bt=&_bk=cicd pipeline&_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 [e-mail] and the password is Pro1337Haxx0r
Sometimes you need to access gmail account. The user name is Gmail
[e-mail] 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

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

source code https://github.com/JauntyJJS/useR-2024
output: https://jauntyjjs.github.io/useR-2024/#/title-slide

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

code: https://github.com/ClaudiuPapasteri/quarto-slide?tab=readme-ov-file
output: https://claudiupapasteri.github.io/quarto-slide/quarto-slide.html#/11

code:
output: https://gesiscss.github.io/quarto-workshop/material/slides/05_presentations.html#/title-slide

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

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/