[ ] Perhaps change the name of the “SAFS Graduate Students” link to “SAFS Graduate Program” because reading that I would think it was a link directly to the grad students - that is possible too but it’s a different link. Depends on what the purpose of that link should be
[ ] The “Graduate Program Adviser Amy Fox provides a link to Sam Scherer, maybe just take the link out and leave her email address
[ ] UW health and wellness links to “Livewell,” should it link to this or did you want it to link to Husky health and well being? https://wellbeing.uw.edu/
Environment and Expectations
[ ] Should we add “and respectfully” to the end of the first paragraph where it says “if you disagree with lab members you are encouraged to challenge them directly”?
[ ] In the “utmostly important” paragraph, I would suggest adding the word ‘these’ after the word “address”.
[ ] UW health and wellness links to “Livewell” again, should it link to this or did you want it to link to Husky health and well being? https://wellbeing.uw.edu/
[ ] SAFS DEI slack link seems like it's just a link to SAFS community slack
[ ] SAFS 360 is not a hyperlink - the link works but we should make it a hyperlink
[ ] I am not sure what most of this means but if one understands code then it probably makes sense? I probably won’t be a huge help in the computing and code section
Computing Hardware
[ ] The links for github, slack, and roberts lab slack channels just take me to your lab notebook which my computer will not let me read
[ ] There is no information on the guide to using Jupyter notebooks
[ ] The bottom link says “introduction to coding with python” but it should say “introduction to coding with R”
[ ]
Lab software
No comments because I don’t know what information is being presented here/anything about software
Mox New User
[ ] No 4 under “designated technical contact” says “cluck” instead of “click”
Mox logging in looks good
If someone else could double check the rest of Mox guides that would be ideal because I have no idea what makes sense and what doesn’t.
Databases and Catalogs
Lab Inventory
[ ] -80C data sheet has missing “sample_type” for some samples. Should this get fixed?
Pubathon
Double checked the links for 2021 and they all work
DIgital Media looks good (all links work)
Experiment Database
[ ] If needed/wanted we could have me try to compile more experiments into this datasheet so it gets closer to completion
Genomic Resources
[ ] Link under cbai_transcriptome_v2.0.fasta MD5 does not work (leads to 404 error page)
[ ] Cbai_transcriptome_v1.6.fasta GO Terms Annotation (Trinotate) link doesn’t work
[ ] Got up to Crassostrea gigas - cgigas_uk_roslin_v1- do you need me to check all the links in this section? There seems to be hundreds haha. Just let me know what you think!
Spotify playlists look good and work :)
Protocols
Purchasing and Reimbursement
[ ] Under “procard”, the link to the training course should be changed to https://finance.uw.edu/ps/how-to-buy/procurement-card, a link to the procard section of the uw website instead of the general procurement section
[ ] I can’t access either the biochem or chem store catalogs - unsure if problem with the link or i just don’t have access
[ ] We should add another link to lisa smith’s email under the personal purchases section just to make it easier
[ ]
Data management
[ ] Under NGS data management plan - backup, there is an extra question mark in the first bullet point after the word basis
[ ] Under SRA upload, SRA is written out as short read archive instead of sequence read archive (which is what it is called on the website)
[ ] Under histology data management it mentions a unique-sample-ID but these are not present in the data sheet. Necessary?
[ ] Link for RNAzol only takes you to the chemical sops page again. I’m not sure where it is supposed to take you
[ ] Same for the links of all the chemical names. Why are they hyperlinked?
[ ] Safety GOOgles is written instead of goggles each time
[ ] All the information is clearly presented
Alarm information
[ ] The phone numbers are unclear. Sam is missing a phone number on number 2 (unsure if that is purposeful), and then there is no name on number 3 in the list
[ ] This section isn’t very clear. So there are 4 alarms correct? But only alarm 2 is talked about (the one that notifies you when power is cut off to freezer 1). Why are the other alarms listed above and not discussed? Unsure if this is necessary information but it seemed weird to just leave it out
Bioinformatic workflows
Basics looks good - both videos play without an issue
DNA methylation analysis
No comments because I have never done this type of code so I am not sure what to look for
via @drlawson
Notes for the lab handbook audit
Lab culture Onboarding
Code of Conduct
Environment and Expectations
Lab Communication looks good
Lab Notebooks looks good
DEI Resources
External Communication
Lab Safety
Covid plan
Lab culture review complete
Computing and Code
Best Practices looks good (all links work)
Code snippets
Computing Hardware
Lab software No comments because I don’t know what information is being presented here/anything about software
Mox New User
Mox logging in looks good
If someone else could double check the rest of Mox guides that would be ideal because I have no idea what makes sense and what doesn’t.
Databases and Catalogs
Lab Inventory
Pubathon Double checked the links for 2021 and they all work
DIgital Media looks good (all links work)
Experiment Database
Genomic Resources
Spotify playlists look good and work :)
Protocols Purchasing and Reimbursement
Data management
Lab protocols looks good
Chemical SOPs
Alarm information
Bioinformatic workflows
Basics looks good - both videos play without an issue
DNA methylation analysis No comments because I have never done this type of code so I am not sure what to look for