https://github.com/al2na/the-world-of-faculty

resources for faculty

https://github.com/al2na/the-world-of-faculty

Repository

resources for faculty

https://github.com/al2na/The-world-of-faculty/blob/master/

# The-world-of-faculty

* [Tips for negotiating salary and startup for newly-hired tenure-track faculty](https://dynamicecology.wordpress.com/2017/03/01/tips-for-negotiating-salary-and-startup-for-newly-hired-tenure-track-faculty/)

* [Ten Simple Rules to becoming a principal investigator](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007448)

Some resources for faculty postion application and grants writing.

* [A list of publicly available grant proposals in the biological sciences](https://jabberwocky.weecology.org/2012/08/10/a-list-of-publicly-available-grant-proposals-in-the-biological-sciences/)

* [My faculty job application materials](http://pgbovine.net/faculty-job-application-materials.htm) from Philip J Guo, a faculty at UCSD.

* [applying for a faculty position](http://effortreport.libsyn.com/15-applying-for-a-faculty-position) by Roger Peng.

* [How to Turn A Good Proposal Into An Excellent Proposal in Eight Admittedly Arduous Steps](https://hopejahrensurecanwrite.com/2014/06/02/how-to-turn-a-good-proposal-into-an-excellent-proposal-in-eight-admittedly-arduous-steps/)

* [Ten simple rules for structuring papers](http://biorxiv.org/content/early/2016/11/28/088278)
* [open grant](https://www.ogrants.org/) find other people's grants.

* [The CommKit](http://mitcommlab.mit.edu/broad/use-the-commkit/) is a collection of guides to successful communication in the biological sciences, written by the BRCL Fellows.

* 
In 2004, my postdoc advisor @DaphnePreuss asked me to write a 1page paper writing guide for the lab, from an advisee point of view (udpated) pic.twitter.com/9akUIOjtNs
— Ravi Palanivelu (@rpalaniveluaz) March 6, 2017


![](https://github.com/crazyhottommy/The-world-of-faculty/blob/master/paper-writing-guide.jpg)

### Stay in the current of literatures.

* [Pubchase](https://www.pubchase.com/)
* [SciReader](http://www.scireader.org)
* [meta](https://meta.org/)
* [citeulike](http://www.citeulike.org/)
* [semanticscholoar](https://www.semanticscholar.org/) managed by Allen Institute for Artificial Intelligence
.
### submit to journals and funding agencies

* [writing in sciences stanford online course](https://www.coursera.org/learn/sciwrite/)
* [AuthorArranger: Conquer journal title pages in seconds](https://authorarranger.nci.nih.gov/#/)
* [typeset](https://www.typeset.io/) Adhering to fuzzy journal guidelines is every researcher's nightmare. Not anymore! 
Introducing Typeset - an intelligent editor that lets you automatically format or re-format to over 14,000 journals with 100% compliance. No fuss. And that's just the beginning...
* [NIH grant podcasts](https://grants.nih.gov/news/virtual-learning/podcasts.htm)
* [how to write a K99](https://k99.sbamin.com/) by Samir Amin (my good buddy). Go and check out this treasure.
* [seeking the k99](https://timoast.github.io/blog/seeking-the-k99/) a blog post by Tim Stuart.
* [citeomatic](http://labs.semanticscholar.org/citeomatic/) find other relative citations you may miss.

* How to write a proposal  

![](https://github.com/crazyhottommy/The-world-of-faculty/blob/master/proposal.jpg)

* [cocites](http://www.cocites.com/)
* [connected papers](https://www.connectedpapers.com/)
* [Citeomatic](http://labs.semanticscholar.org/citeomatic/)  finds new citations for you.
* [Ten simple rules for structuring papers](http://www.biorxiv.org/content/early/2017/05/23/088278)
* [NIC guide](https://www.niaid.nih.gov/grants-contracts/write-research-plan)
* [Thoughts on reviewing NIH proposals: What is the difference between a 2.0 and 3.0 in initial score?](http://mistressoftheanimals.scientopia.org/2018/02/10/thoughts-on-reviewing-nih-proposals-what-is-the-difference-between-a-2-0-and-3-0-in-initial-score/) a blog post.

* [ZoteroBib](https://zbib.org/) is a free service that helps you quickly create a bibliography in any citation style.

* [How to craft a figure legend for scientific papers](https://blog.bioturing.com/2018/05/10/how-to-craft-a-figure-legend-for-scientific-papers/) 

### Time planning
* [Time is Citations: How I Plan My Days](https://olgabotvinnik.com/blog/time-is-citations/) A post by Olga Botvinnik in  UCSD on how she manages her day. I learned a lot!

* [how to manage a lab](http://www.labmanager.com/management-tips)

### review a paper

* https://github.com/jtleek/reviews by Jeff Leek.
* [A Guide to Responding to Scientific Peer Review](https://jef.works/blog/2020/06/17/responding-to-scientific-peer-review/) by Jean Fan.



### Data plan
* ["All you need to know about data management plans"](https://zenodo.org/record/803756#.WWelz9PyvUo) - workshop for Principal Investigators in Bioinformatics
### Teaching
* [How to Teach Programming (And Other Things)](http://third-bit.com/2017/05/31/how-to-teach-programming.html) by Greg Wilson.
* [Teaching Tech Together](http://teachtogether.tech/) by Greg Wilson as well.

### fundings

* [Early Career Funding, Awards, and Other Funding](https://docs.google.com/spreadsheets/d/1H1aj--VUYr7eMFk_T7x0Oh985LqbyyscXg2wAAevDnU/edit#gid=0) 
* https://ecrcentral.org/resources
* [Funding schemes for postdoctoral fellowships](https://asntech.github.io/postdoc-funding-schemes/)
* [Postdoctoral Funding Opportunities by Johns Hopkins](https://research.jhu.edu/rdt/funding-opportunities/postdoctoral/)
* [Early Career Funding Opportunities by Johns Hopkins](https://research.jhu.edu/rdt/funding-opportunities/early-career/)

### manage a lab

* [Ten quick tips for making things findable](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008469)
* [Making experimental data tables in the life sciences more FAIR: a pragmatic approach](https://academic.oup.com/gigascience/article/9/12/giaa144/6034785)
* protocols: https://www.protocols.io/
* [electronic lab notebooks review by Harvard HMS](https://datamanagement.hms.harvard.edu/electronic-lab-notebooks)
* [Rspace](https://www.researchspace.com/) Next-gen Elab notebook.
* [How to grow a healthy lab](https://www.nature.com/collections/pmlcrkkyyq)  Nature collections
* [Bench Sci](https://www.benchsci.com/) Run Successful Experiments with the Right Antibody. Let our AI decode the literature to provide antibody usage data that's unbiased and experiment-specific

### collabration

* Rule #1: Say no unless you are excited. ---Credits to Shirley Liu and Stan Gu.
* [The ASCCR Frame for Learning Essential Collaboration Skills](https://www.semanticscholar.org/paper/Essential-Collaboration-Skills%3A-The-ASCCR-Frame-for-Vance-Smith/8ddb0800fbf0a43e343809f9df92fe622b25f3f5)

### recruiting

### training

* [Ten simple rules for making training materials FAIR](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854)

### conferences

* [Conferences & Schools 2019](https://generegulation.org/conferences-2019/)
* [conferences by nextgenseek](http://nextgenseek.com/ngs-conferences/)

###  collaborative writing

* [Synchronized editing: the future of collaborative writing](https://www.nature.com/articles/d41586-020-00916-6)
* [manuscripts](https://www.manuscripts.io/about/)
* [Open collaborative writing with Manubot](https://manubot.org/)
* google doc + paperpile


### digital tools for organizing a computational biology lab

collected from this twitter thread https://twitter.com/tangming2005/status/1230568527033012225

* [basecamp](https://basecamp.com/) for tracking progress of projects. Github integration using [zapier](https://zapier.com/home)

"We use Basecamp in my lab, with GitHub integration via Zapier" -- Naupaka Zimmerman

"We use basecamp at HBC, it helps to track progress, n communicate with collaborator. For code tracking we use github. Though for my personal use, I hv jupyter notebook for code, Evernote for docs,and full Analysis I build docker for each project. This gives me peace" -- Preeti Aahir

* [github + zenhub](https://www.zenhub.com/) project management for github.
"We're trying out gitbook for the group documentation and working policies, etc. In addition, we use @ZenHub
 because of its tight GitHub integration to track projects" -- Moritz E. Beber
 
* [trello](https://trello.com/en-US) group working, organize projects.

"I use Trello for organisation and push my collaborators to use it. It helps keeping tasks, code, input, output & comments organised. We have common conda envs on the cluster and a place to store scripts. GitHub would be better for scripts but it's a lot to learn for some people."

"But I think that everything could be moved to @trello with a github integration and links to input data on shared folders on the HPC (so that large files are not stored on the Trello boards). Also it's free (compared to http://Monday.com)."

--Gautier Richard

* [Notion](https://www.notion.so/) All-in-one workspace.
"We have a general lab section with boards for expectations, on boarding, and getting started with the HPC. Each trainee then has their own long term goals boards and separate projects board." -- Nicholas Mancuso

* [github wiki](https://help.github.com/en/github/building-a-strong-community/about-wikis) for documenting projects.

"Recently commenced attempt at this is to use a github repo with the wiki as the guide (onboard routines), and possibly the repo itself for useful scripts" --Kieran Campbell
 
* [gitbook](https://www.gitbook.com/) for other documenting purposes. onboard routine: e.g. HPC setup. pipeline running.

"We're trying out gitbook for the group documentation and working policies, etc. In addition, we use @ZenHub
 because of its tight GitHub integration to track projects" -- Moritz E. Beber
 
* [electronic lab notebooks](https://datamanagement.hms.harvard.edu/electronic-lab-notebooks) wetlab usage as well.

* [knowlege repo from airbnb](https://github.com/airbnb/knowledge-repo)
"We are deploying airbnb's knowledge repo as proof of concept and are enjoying it so far. Let me know what you think!" -- An Hoang.

* [discord to replace slack?](https://discordapp.com/)

* [super-productivity](https://github.com/johannesjo/super-productivity) Free to do list & time tracker for programmers & designers with Jira integration. 
read https://bioinformaticsworkbook.org/projectManagement/Intro_projectManagement
and https://olgabotvinnik.com/blog/time-is-citations/

* [The Beginners Guide To Scrum And Agile Project Management](https://blog.trello.com/beginners-guide-scrum-and-agile-project-management)

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