Note: BrainArch is intended for studying and sharing knowledge about neuroscience, bioinformatics, and related fields. It is not intended for commercial use.
At the currect stage, documentation is available in the Blogs menu, and tools can be found under the Tools menu. Additional features will be rolled out soon.
Have an idea? I’d love to hear it — share it with me!
Always start by reading the relevant documentation; if you need further guidance, just let me know and I’ll post a guide.
Please visit Galaxy Blogs to have an overview about available internal resources for data management, analysis, visualization, etc.
Internal links
Below is a list of internal links (i.e., they cannot be visited outside the internal network and can only be used internally):
Ubuntu server:
172.16.50.209. You should access it via an SSH client (for both data analysis and file transfer) or an SFTP client (for file transfer only). Before connecting via SSH, verify that you have bash login permission.NeuroBorder Shiny Web App: https://172.16.50.209/r-shiny/neuroborder/.
NeuroBorder Galaxy: https://172.16.50.209/galaxy/neuroborder/.
Access RStudio in a web browser: https://172.16.50.209/rstudio/server/.
Archive directory: https://172.16.50.209/archive/. This is used to share some data internally. Any members can upload their data to here.
Database directory: https://172.16.50.209/database/. This is used to share some (biological) data internally. Any members can upload their data to here.
Synology NAS: http://172.16.50.55:5000/.
Below is a list of links for various purposes:
Metascape: https://metascape.org/gp/index.html#/main/step1. You can perform various annotation analyses over a gene set like GO enrichment analysis. It can cluster significantly similar GO terms together when you perform GO enrichment analysis. This is quite useful for picking interesting GO terms from an extensive list of GO terms.
g:Profiler: https://biit.cs.ut.ee/gprofiler/gost. Used for ORA (Over-Representation Analysis) or GSEA (Gene Set Enrichment Analysis) (Recommended).
Enrichr: https://maayanlab.cloud/Enrichr/. The same as g:Profiler.
DAVID: https://davidbioinformatics.nih.gov/. The same as g:Profiler.
GSEA official: https://www.gsea-msigdb.org/gsea/index.jsp.
Comparative Mammalian Brain Collections: https://brains.anatomy.msu.edu/museum/brain/.
WashU Epigenome Browser: https://epigenomegateway.wustl.edu/.
UCSC Genome Browser: https://genome.ucsc.edu/.
Timetree of Life: https://timetree.org/home.
NIH’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN): https://www.biccn.org/.
Easy use for Windows 10/11: https://www.bilibili.com/opus/904672369138729017/. It provides one of the most convenient ways to disable Windows update for decades.