Useful links (updated: 2024-10-23)

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Public health issue

1.Health Intervention and Technology Assessment Program
http://www.hitap.net/
2.Strategy and Planning Division (Thai MOPH)
Gather all the statistic info related to Thai public health
http://bps.moph.go.th/new_bps/node/232
http://bps.moph.go.th/new_bps/healthdata
3.International Classification of Diseases
https://icd.who.int/

4.WHO Model list of essential in vitro diagnostics

https://edl.medevis.test.evidenceprime.com/

5.Mesothelioma Cell Types

https://mesothelioma.net/mesothelioma-cell-types/

6.สถาบันวิจัยระบบสาธารณสุข - HSRI

https://kb.hsri.or.th/dspace

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For High Content Screening Research

1.Sispharm

http://sisyspharm.org/index.php/en/
2. Free software for High Content Screening
http://hcs-analyzer.ip-korea.org/
3.Columbus data analysis
http://columbus.si.mahidol.ac.th/login?next=/

4.ECDD

http://ecdd.sc.mahidol.ac.th/
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For Database geek

1. Interactome
https://interactome3d.irbbarcelona.org
2. Omic-tools
https://omictools.com/
3.Expression Atlas
https://www.ebi.ac.uk/gxa/home
This one includes the expression profiles of all available species that deposit on the public database. I really like the layout of this website.
4.Bioimage analysis
http://icy.bioimageanalysis.org/
5. Genevestigator
https://genevestigator.com
This is the website used for the gene profiles mapping. I used this one to help me analyze the freely available microarray data that deposited on GEO dataset (NCBI).
6. The human protein atlas
https://www.proteinatlas.org/
To tell us about which protein is up- or down-regulated during carcinogenesis. The website is very up to date.
7. DrugBank
https://www.drugbank.ca/
I have been working with genotoxic compounds and I need to find the information on the solubility of each compound and making the right preparation to treat the cells.
8. Cancer cell line encyclopedia
https://portals.broadinstitute.org/ccle
9. Genomics of Drug Sensitivity in Cancer (GDSC)
http://www.cancerrxgene.org/
10.Cancer Therapeutics Response Portal (CTRP)
https://portals.broadinstitute.org/ctrp/
11.The Library of Integrated Network-Based Cellular Signatures (LINCS)
http://www.lincsproject.org/LINCS/
12.IGRhCellID: integrated genomic resources of human cell lines for identification

http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi
QC-for the human cell line experiment. It is good to check whether the cell lines you are currently working with is authentic.
13.cBioPortal for Cancer Genomics
http://www.cbioportal.org/index.do
This website is extremely good for finding the mutations related to cancer. It is very up-to-date. It also has R-package which you can download and put the command to retrieve the data from the database.

14.COSMIC
http://cancer.sanger.ac.uk/cosmic
the Catalogue Of Somatic Mutations In Cancer -- it is good for knowing the information on mutations of interested gene in all available types of cancer.
15.Oncomine database
https://www.oncomine.org/
16.The cancer genome atlas - TCGA
https://cancergenome.nih.gov/
Tool for retrieving the genome data on the cancers
17.Cancer hotspot mutations
http://www.cancerhotspots.org/#/home
This database provides the information about the frequently occur mutations of genes in cancer. The significant relies on the Q-value (more approaching to zero means very highly associated). It also indicates the type of tumors where the mutations have been found as well as the number of cases.
18.OncoKB: A Precision Oncology Knowledge Base
http://oncokb.org/#/
19.NCI-60
https://discover.nci.nih.gov/cellminer/analysis.do
19.1Cell miner
https://discover.nci.nih.gov/cellminercdb_reviewers/
20.REPAIRtoire
http://repairtoire.genesilico.pl/
A collection of DNA repair protein
21.Online Mendelian Inheritance in Man®
http://omim.org/
An Online Catalog of Human Genes and Genetic Disorders
22.Cell Strainer
https://depmap.org/portal/cell_strainer/
Online tool to check the lineage of cell lines
23.Metabolomics
http://metabolomicssociety.org/
24.WEB-based GEne SeT AnaLysis Toolkit
http://www.webgestalt.org/option.php
Gene annotation and functional analysis
25.Traditional Chinese Medicine Database in Taiwan
http://tcm.cmu.edu.tw/index.php
26.The SCImago Journal & Country Rank
https://www.scimagojr.com/index.php
To check the journal of interest fall into which quartile
27.3-Dimensional Electron Microscopy (EMDatabank)
http://www.emdatabank.org/
Unified Data Resource for 3-Dimensional Electron Microscopy
28.Human Ageing
http://genomics.senescence.info/
29.Open Innovation AstraZeneca
https://openinnovation.astrazeneca.com/clinical-compound-bank.html
30.Cumulus-DSB response kinetics
http://www.dna-repair.live/cumulus/
31.Pharma research
https://www.phrma.org/
32.Cellosaurus - a knowledge resource on cell lines
https://web.expasy.org/cellosaurus/
33.The human metabolome database
http://www.hmdb.ca/
34.Liver toxicity (FDA-drug)
https://livertox.nlm.nih.gov/index.html
35.High-value datasets
https://data.go.th/Default.aspx
36.Drug repurposing (Broad Institute)
https://clue.io/repurposing
37.Therapeutic target database
https://db.idrblab.org/ttd/
38.Biomart
https://biomart.genenames.org/
39.Project Score
https://score.depmap.sanger.ac.uk/
40.Cancer Dependency Map
https://depmap.org/portal/
41.canSAR
http://canext3.icr.ac.uk/
42.Chemical Probes
http://www.chemicalprobes.org/
43.Aspergillus Secondary Metabolites Database (A2MDB)
https://www.iictindia.org/a2mdb/Home.aspx

44.National e-Science Infrastructure Consortium
http://www.e-science.in.th/
45.Medicinal plant (MU)
http://www.medplant.mahidol.ac.th/index.asp
46.Tool for protein bioinformatics
http://xtal.cicancer.org/links/prot-links.html

47.Thai national drug bank

http://ndi.fda.moph.go.th/ndi_home

48.Open Government Data of Thailand

https://opendata.data.go.th/

49.Speeding up scientific knowledge production (checking turn around time)

https://scirev.org/

50.Code biology

http://www.codebiology.org/index.html

51.GWAS

http://www.nealelab.is/uk-biobank

https://www.ebi.ac.uk/gwas/home

52.Brain stuff

https://www.brainfacts.org/

53.The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH)

https://www.ich.org/

54.US-FDA drug check

https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm

55. Archive -- free stuff

https://archive.org/

56.Franklin by Genoox

https://franklin.genoox.com

57.BaseSpace Variant Interpreter

https://variantinterpreter.informatics.illumina.com/home

58.Clinical Interpretation of Variants in Cancer

https://civicdb.org/welcome

59.National Research Index Data

https://www.nrct.go.th/RandDIndex

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Journal ranking

1.Checking the impact factor (through intranet only) -JCR

https://ejournal.mahidol.ac.th/login?url=https://jcr.clarivate.com

2.Checking TCI

https://tci-thailand.org/

3.Checking through SJR

https://www.scimagojr.com/journalrank.php

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Animal model database

1.Fly
There are so many learning tools that we can learn from - it is pretty amazing!
https://flybase.org/
2.Zebra fish
Transparent, external fertilization, vertebrate -
https://zfin.org/
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For diabetic folks

1.The AmericanDiabetes Association

https://www.diabetes.org/

2.Thai diabetes association

https://www.dmthai.org/

3.Diabetes atlas

https://diabetesatlas.org/

4.International diabetes federation

https://idf.org/

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Science communication

1.Thailand research
https://researchcafe.org/
Pretty cool website, TSRI tries to engage the research into the Thai community.

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Visualization

1.Different kind of visualization
http://www.bioinformatics.com.cn/en
Free tools to plot different types of graph.

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Microbiome

1.Quantitative Insights Into Microbial Ecology

http://qiime.org/

2.Microbiome stuff

https://microbiomedigest.com/
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For life long learner

1.Genetics learning
https://learn.genetics.utah.edu/
Pretty cool -- it also has the channel for donation to support the learning.
2.Udemy
https://www.udemy.com/
I have paid for several courses, each course can be evaluated by the ppl who attend the course.
3.Coursera
https://www.coursera.org
There are so many free courses, but if you want a certification then you have to pay.
4.Space CBS
https://space.cbs.chula.ac.th/login/
5.MU-EdX
https://mux.mahidol.ac.th/

6.MUx

https://mooc.mahidol.ac.th/
7.STAT365 - easy explanation

https://365datascience.com/

8. Open knowledge repository

https://openknowledge.worldbank.org/

9.Disease control priorities

http://dcp-3.org/

10.Chemistry Library -- a very cool website to explain chemistry!

https://chem.libretexts.org/

11. โรงเรียนไท

http://libertyschool.in.th/public/

12. National Institute for Child and Family Development

https://nicfd-member.mahidol.ac.th/member/login

13. Lab Exchange

https://www.labxchange.org/

14. Khan Academy

https://www.khanacademy.org/

15. Research Academy Elsevier

https://researcheracademy.elsevier.com/

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For signaling nerdy!!

1. Only for TP53 or p53
http://p53.iarc.fr/Default.aspx
Since p53 is the protein that plays key important roles in cellular processes; cell cycle, apoptosis, and DNA repair etc.
2.Only for Wnt
http://web.stanford.edu/group/nusselab/cgi-bin/wnt/
Not only wnt has been related to proliferation, differentiation, and polarity. Recent evidence has shown that it also links to the DNA damage response.
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For self-study computer language and data science

1. R-language
https://www.r-bloggers.com/

1.1 Cheatsheet for R-package

https://rstudio.com/resources/cheatsheets/

1.2 R-notebook

https://bookdown.org/yihui/rmarkdown/
1.3 Working with R on cloud

https://rstudio.cloud/

2. R, phyton, SQL
https://www.datacamp.com/
some courses are free and some courses need to pay
3. Stang library data science, Faculty of Science, Mahidol University
http://stang.sc.mahidol.ac.th/it/datascience.php
I am always appreciated for the service and enthusiasm of the staff over there. Now, they collect the websites which ppl can self-educated wherever they want and also the coding material which is now increasingly important since we live in the world of big data!
4. Stackoverflow
https://stackoverflow.com/
For putting the questions//share the knowledge on the coding materials.
5. Collection of python package
https://pypi.org/

6. Kaggle

https://www.kaggle.com/

7. Weka (online tool on data mining)

https://www.cs.waikato.ac.nz/ml/weka/
8. Scikit-learn (python based)

https://scikit-learn.org/stable/index.html#

9. Statistical data analysis with R

https://stat.ethz.ch/R-manual/R-devel/doc/html/index.html

10. AutoML

https://www.automl.org/automl/

11. AIforThai

https://aiforthai.in.th/

12. Git Repositories with bioinformatics training material

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

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GPT3-related application

1.Elicit

https://elicit.org/

2.Paper-digest

https://www.paper-digest.com/

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For Synthetic biology

Cellular engineering on yeast!
http://syntheticyeastresource.com/
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For Imaging people
I use this fluorescence microscopy quite often lately. There are so many sources that I think it is very useful to read and do the self-study.

1. Image J
https://imagej.nih.gov/ij/
Free tool to analyze the imaging data
2. Cell Profiler
http://cellprofiler.org/
This is also the free tool that you can write up your own pipeline and analyze the array of images. Plus there are the webboards that are very interactive and helpful for finding the prototype pipeline to asking for help or fix your pipeline to run the analysis.
3. CellProfiler Analyst
http://cellprofiler.org/cp-analyst/#
Still figuring it out how to use it, since it can be applied to the machine learning to sort out some unwanted nucleus morphologies.
4. Fluorescence protein picker tool
https://www.fpbase.org/
I have been recommended during the talk on High Content Screening at SI
5. Image Forum
https://forum.image.sc/

6. Finding knowledge related to microscope

https://www.pepleroptics.com/

7.Spectra viewers

https://www.thermofisher.com/order/fluorescence-spectraviewer

8. Global imaging

https://globalbioimaging.org/

9. BioImaging North America

https://www.bioimagingnorthamerica.org/

10. Molecular expression (fundamental knowledge of microscope!)

https://micro.magnet.fsu.edu/primer/index.html

11. Eurobioimaging

https://www.eurobioimaging.eu/

12. Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy

https://quarep.org/

13. Integrative Imaging (Advanced Imaging Center, Janelia HHMI)

https://www.i2janelia.org/

14. Advanced imaging center

https://www.aicjanelia.org/

15. A list of useful microscopy resources (suggested by AIC, Janelia HHMI)

https://www.janelia.org/support-team/integrative-imaging/additional-information

16. Melbourne Advanced Microscopy Facility

https://microscopy.unimelb.edu.au/om/capabilities/workshops-resources

17. Educational website for learning basic microscopy with certification!

https://microtutor.globalbioimaging.org/

18. Singascope

https://www.singascope.sg/

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For Chemoinformatics ppl
There are three programs which I have been suggested by my colleagues.

1.ChemDes
http://www.scbdd.com/chemdes/
2.PaDEL-Descriptor
http://www.yapcwsoft.com/dd/padeldescriptor/
3.Datawarrior
http://www.openmolecules.org/datawarrior/
4.Good lectures funded by Horizon

http://bigchem.eu/

5.Pybiomed

https://pybiomed.readthedocs.io/en/latest/index.html#
Rich of packages to extract the molecular features from small molecules, protein, and nucleic acids

6.Personal blog but passionate on chemoinformatic

https://data-professor.medium.com/

https://drzinph.com/

https://practicalcheminformatics.blogspot.com/ (Pat Walters)

https://rdkit.blogspot.com/

https://www.peter-ertl.com/

7.Chemicalize (online drawing chemical structures)

https://chemicalize.com/

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Genome editing research

1.The SCGE program

https://scge.mcw.edu/

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Microscope
There are four brands that I use often time to learn more about the fluorescent microscope principle.

Nikon
https://www.microscopyu.com/
Olympus
https://www.olympus-lifescience.com/en/microscope-resource/

https://lifescience.evidentscientific.com.cn/en/microscopes/
Leica
https://www.leica-microsystems.com/science-lab/
Zeiss
https://www.zeiss.com/microscopy/int/solutions/life-sciences.html

https://zeiss-campus.magnet.fsu.edu/index.html
Microcourses (all about microscope)
https://www.youtube.com/c/Microcourses/featured
Microscope opensource software
https://www.openmicroscopy.org/index.html

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Staining issue

1.IHC world - a collection of vendor and knowledge, also discussion
http://www.ihcworld.com/index.htm
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Education research

SHEE consult -- free of charge

https://shee.si.mahidol.ac.th/index.php/th/menu-th-3/shee-consult

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Tool for biological calculation

Serial dilution
http://fluffyfrog.net/calc/
Calculate roughly how many round-shaped cells fit in the well
https://www.engineeringtoolbox.com/smaller-circles-in-larger-circle-d_1849.html

Calculation for reagent preparation

https://www.medchemexpress.com/molarity-calculator.htm
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Inventory and infrastructure

1.List of organizations, products & services in the biotech industry
http://www.biotechthailand.com/
2.Antibody vendors
http://antibodyregistry.org/
My work deals with more than one species, so the information on this website is very helpful for my work.

3.Non-commercial antibody price

https://dshb.biology.uiowa.edu/
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Fraud check and research integrity

1.Forbetterscience
https://forbetterscience.com/
2.Retraction watch
https://retractionwatch.com/

3.COPE

https://publicationethics.org/

4.Pubpeer

https://pubpeer.com/static/about

5.The office of research integrity

https://ori.hhs.gov/

6.Retraction database

http://retractiondatabase.org/

7.Science Integrity Digest

https://scienceintegritydigest.com/

8.Research Ethic from University of Minnesota

https://www.ahc.umn.edu/img/assets/26104/Research_Ethics.pdf

9.Predatory report

https://predatoryreports.org/

10.NORWEGIAN REGISTER FOR SCIENTIFIC JOURNALS, SERIES AND PUBLISHERS

https://kanalregister.hkdir.no/publiseringskanaler/Forside
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Patent search
Some are free and some have to pay in order to get access, asking the innotech in each university will provide the time-limited account to search for the patent. Each tool will have a different platform which users can play around and learn what the current trend is and whether the topic, he or she would like to do the research has the uniqueness that can be patentable.

1.Lens (free)
https://www.lens.org/
2.DIP (free) - Thai
http://patentsearch.ipthailand.go.th/
3.Patsnap (limited user ask innotech) - large database
http://www.patsnap.com/
4.Espacenet Patent search (European)
https://worldwide.espacenet.com/
5.World IP
http://www.wipo.int/portal/en/index.html
6.Google patent
https://patents.google.com/

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Diagnostic test kit

1.FIND

https://www.finddx.org/

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Academic writing

1.Scribbr

https://www.scribbr.com/

2.Essaysoft

https://www.essaysoft.net/index.html

3.English example sentences

https://ludwig.guru/