Lab:labinfo

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Welcome, Ren Lab Members!

 

General Information

Lab Website

https://biomol.bme.utexas.edu/  

Lab Office Number

BME 3.516

How to Find Lab

  • Go to the 3rd floor of BME (ground floor on Dean Keeton side, next floor up on the South side)
  • There is a hallway on the west side of the building that runs north-south
  • if you come in from the lobby it is on the right side of the building running straight back
  • the last door at the end of the hallway (located near Stair 3)

Dr. Ren's Office Number

BME 5.202M (located in 5th floor faculty suite)

Communication and File Sharing

Slack

  • utren.slack.com
  • accounts will be created for new lab members/rotation students
  • noteworthy channels
      1. software for discussing various lab software + issues
      2. cat for sending cat pics
      3. paper-literature for sharing helpful papers + interesting new general papers
      4. amoebaplus
      5. poltype
      6. general - general Ren lab stuff
      7. allinclude - basically general but including some Schnieders lab members

Lab Contacts

https://docs.google.com/spreadsheets/d/1Lea3_EAsVyOcMja7Ox_mNfj8ZNzj6Dupd8w5dNuFr4I/edit?usp=sharing

Lab Meetings

https://docs.google.com/spreadsheets/d/133vg99syg17xPR-H-UH0B2gLlC9469AFAwMQx2LGn4s/edit?usp=sharing

Individual Meetings

https://docs.google.com/spreadsheets/d/1yLw5xenlOgIdsylFVk4fDnu7s5juZvgFgU8ztYvMfQE/edit?pli=1#gid=0  

Cluster Sign-Up Sheet

https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit?pli=1#gid=0 

AMMM Meeting Sign-Up Sheet (Summer)

https://docs.google.com/document/d/1Pn2ZhHBQ82miVhl6CGG0zj2rMQxTLvTznrGColcNYhQ/edit?usp=sharing

Suggested Literature (in Box)

https://utexas.app.box.com/folder/103794407727  

Learning and reading

You are expected to learn from your labmates and by reading literature regularly. Most learnings in grad school/postdoc training are not from classroom!

You will run MD simulations and free energy calculations, using polarizable force field AMOEBA. These are expertise our lab has developed over past two decades so anyone to graduate from this lab should understand how and why on the following relevant subjects. You all should spend time read papers and documents I have been sharing. If you don't understand what you do and only run others' scripts to get numbers, you won't go far.

  • Polarizable multipole force field AMOEBA. why and how
    • Understand AMOEBA model (read slides and latest review paper Jing et al)
    • Using POLTYPE to get parameters and understand what POLTYPE is doing (read POLTYPE papers)
  • Hydration free energy. Salt effect and charge correction (if solute has net charge)
    • FEP and BAR
    • Other methods including TI and WHAM (PMF)
  • Binding free energy calculations
    • restraint and standard state correction
    • Neutralizing counter ion and background salt; what to do when ligand has net charge
    • It is OK to use other's script (Brandon, CW) to set thing up and learn. But you need to know what the program is doing, how and why again.
  • How to compile Tinker CPU and GPU code

Many topics above found on lab wiki (https://biomol.bme.utexas.edu/tinkergpu) and a BOX folder I shared with lab members (for example AMOEBA folder has slides and papers introducing AMOEBA). If you don't have/see anything or have question, contact asap. It is important to establish a routine, setting aside time to read regularly (daily, weekly). I would start from basic and whatever relevant to what you are doing now and gradually cover more and more.



Lab policy & resource

Financial support

PhD students are typically fully supported via either GRA ot TA. However funding is not always guaranteed. Studenst and postdocs are expected to work deligently and be productive, which in turn will help us to secure the funding to support your stipend, fringe, tuition and other expense.


Work schedule

Postdocs are required to fill in time sheet per university policy. While we don't require everyone follow a fixed schedule, everyone is expected to follow "reasonable" working hours (e.g. 9am - 5pm). People who show chronic tardiness and fail to comply after multiple warnings will be asked to leave.

Vocation and leave

Graduate students and postdocs are supported by either state or federal funds (including TA and RA ship). You are considered employees (hence the benefit etc.). We typically observe the university official holiday and vacation policy (http://www.utexas.edu/hr/holiday/ and http://www.utexas.edu/hr/current/leave/annual.html). You are allowed to take 4 weeks off for vacation each year, holidays and sick days not included. Please consult with PI in advance to plan on a vacation.

Please noteWinter, spring and summer breaks are NOT vacation time. These are breaks for classes and undergraduate students, not for staff and employees. You can certainly take vacations during the breaks (use against the 4-week a year vacation time).

You need to consult with PI for longer/extended leave. You may not expect financial support for the extended leave.

We expect students to respect the rules and work diligently, which is essential for us to to receive funding to support everyone in the lab.

Lab Resource

When use the cluster, be considerate. Don't spread your job all over the nodes (use all the processors on one node before using other nodes), so that others that need the multiprocessors can utilize them.

CPU & GPU resources in the lab (email Dr. Ren if you need write permission) https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit#gid=0

More about using the cluster: https://biomolmd.org/mw/index.php/Lab:newuser

Lab Responsibility

Each of you will share some lab responsibility, such as maintenance, purchasing, organizing group meeting etc. Senior lab members are expected to advise and help out new lab members on research.

Lab security

  • Do not use university resource for personal use.
  • Do not install or alter operating system and software, change system setting or have root privileges (including sudo) on lab computers/workstations/laptops, unless with explicit permission from PI.
  • You are responsible to make sure your workstation and user account (password) are secure.
  • The university monitors the internet activity of every network port.


Always lock the door when you are the last one to leave.

Meetings and Conference

  • Funding

The lab provides support for each of you to go to meetings and conferences to present your work in orals or posters. The amount ($500 - $1000 a year) depends on funding availability and your presentation (oral has higher priority) etc. You are also strongly encouraged to seek for support from department, college and society etc, many in the format of award.

Oral presentations receives a higher priority for support than posters.

  • Save all your receipts and program documents etc.
  • Send me the following in electronic format (word doc, PDF)
    • Your abstract before submission for me to check
    • Published abstract (web print or scanned pdf)
    • Official program page that has your presentation or poster title and author names (web print or scanned pdf is fine).
    • The final powerpoint files for presentation or poster

Graduate students fellowships

http://www.grad.nd.edu/gfd/

http://www.lib.msu.edu/harris23/grants/3gradinf.htm#a


NSF, https://www.nsfgrfp.org/

NIH, https://researchtraining.nih.gov/programs/fellowships/f31

America Heart Association https://professional.heart.org/professional/ResearchPrograms/ApplicationInformation/UCM_443316_Predoctoral-Fellowship.jsp

SAMRT: https://www.asee.org/fellowship-programs/graduate 

NDSEG https://ndseg.asee.org/ 

 

Fellowship Databases:

https://gradschool.cornell.edu/fellowships 

https://awardsdatabase.usc.edu/

http://grad.berkeley.edu/news/headlines/guide-to-fellowships-grants/ 

Technical reading materials

Molecular Modeling

Book: Molecular Modelling, Principles and Pllications, Andrew Leach
Computer simulations of liquids, Allen & Tildesley
Book: Molecular Simulations, Frenkel and Smit

You can use Google to find these books online.

 

Free energy

Book: 

Free energy Calculations, Theory and Applications in Chemistry and Biology, Chipot and Pophorille, Springer

Review by Simonson & Roux (charge correction/solution-gas-phase): Concepts and protocols for electrostatic free energies 

https://utexas.box.com/s/fx8ixqhz9zj9i5ebv3rzrgclwiighnd6

More about charge corrections when system/ligand being disappeared is not neutral 

https://utexas.box.com/s/nj6jcufmms5hs1xqu5pywkwp3kax3y6k

Force Fields

MSI force field handbook: 

 https://utexas.box.com/s/ge7f4q6svq5ammy736c7d729ms6jxzzw

Molecular binding termodynamics & simlations

Gilson & Zhou 

 https://utexas.box.com/s/esttb5govnir7mvnvydcid4ukv7nxmnc
 https://utexas.box.com/s/dugh8ba95gf8v0fnsnzf6a63beu47qee
 https://utexas.box.com/s/p2fcjdzdssuxicopv5mkl843grrjinoh

Hamelberg & McCammon 

 https://utexas.box.com/s/bsayz0jmfgd7o8ibx0pqtkoqwuk108tm

Ren lab: 

 http://www.pnas.org/content/pnas/105/17/6290.full.pdf

Data analysis

R for Data Science: http://r4ds.had.co.nz/

Writing

Writing a scientific paper, step by painful step by Kevin D. Lafferty

 http://trophiccascades.forestry.oregonstate.edu/sites/trophic/files/Lafferty_WritingScientificPaper.pdf

Recipe for a Quality Scientific Paper: Fulfill Readers and Reviewers Expectations

Prof Yaoqi Zhou https://utexas.box.com/s/m93b92gwzcxgi1iw8qw7gdf6z7duzmm1

Making better figures

 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833

21 suggestions

https://www.scitechedit.com/images/21_writing_tips.pdf

Ten simple rules for structuring papers

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619

 

Literature search

pubmed: https://www.ncbi.nlm.nih.gov/pubmed/ 

Web of science (use UT eid when off campus): https://guides.lib.utexas.edu/az.php?a=w 

Hot paper search https://www.oligotherapeutics.org/hot-papers-search/

Off campus access to paper download via ezproxy: https://legacy.lib.utexas.edu/help/proxy.html#subscription

Check out resources (including classes) offered by university library

Presentation

http://blogs.nature.com/naturejobs/2017/01/11/scientific-presentations-a-cheat-sheet/

http://www.nextscientist.com/improve-presentation-skills-of-phd-students/

 

Career Development

The Professor Is In: The Essential Guide To Turning Your Ph.D. Into a Job

https://www.amazon.com/Professor-Essential-Guide-Turning-Ph-D/dp/0553419420

Some contents are inspired by https://twitter.com/thehauer/status/1021179403680862218?s=19

Communication kit

nstructions on writing cover letters, formatting CVs, writing abstracts, personal statements, etc.

http://mitcommlab.mit.edu/be/use-the-commkit/

Lab Resources

Disk spaces

Your home dir is in /home/YOURUSERNAME, which is physically on Nova and space is limited. But each of you have space in /work/YOURUSERNAME (physically on SUN), which is at least 2 TB (more if needed). You can access home and work dir similarly on all computers in the lab. If you have MD jobs producing large trajectories and you wan to keep them for analysis (until paper pub), please use /work. You can check your space and quota limits in /opt/quota.* Once you reach quota you can not log in or execute commands.

Using Lab Cluster

new user set up to access lab cluster

Cluster Monitoring

https://biomol.bme.utexas.edu/~pren/nodes.html

CPU & GPU resource sign up

GPU Monitoring

https://biomol.bme.utexas.edu/~rq875/checkgpu.log  

Tinker Tutorials

https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut    

Poltype Github

https://github.com/TinkerTools/poltype2

Linux Utilities

https://docs.google.com/document/d/1cnmSItdRXDBcpVBGhwDahJVJ2jeh4l2oDVpMBLtlySE/edit  

Lab Guide for Grad Students

https://docs.google.com/document/d/1PKyWNTntusPeRrOiGaLAkUvJbuuc4cVBfE4Lo9ZMt2I/edit    

UT Resources

Ombuds

Employee Assistance Program

Counseling

Wellness (sometimes has fitness videos)

Night rides (Lyft discount)

University Health Services

COVID testing

Women’s Health

Free nurse advice line

Student Emergency Services

Services offered https://deanofstudents.utexas.edu/emergency/howwecanhelp.php 

Student Emergency Fund

Services for Students with Disabilities

Life in Austin

Coffee Shops

Food

Essential Stores

 

Outdoor Landmarks / Hiking

Highest point in Austin, not much of an actual hike

Pennybacker Bridge (park on side of road, can go up either side of road)

Overlook Trail (3ish miles each way, nice overlook part way, decent elevation change)

Bat Observation

  • https://goo.gl/maps/ZHfnn54qKY6icEq3A
  • Austin has a bat colony. The bats migrate but they like to hang out under the Congress bridge.
  • You can park in a paid lot or take the bus and watch the bats fly sometime around sunset. You can also watch the bats from the river or on top of the bridge.
  • It’s really neat and an Austin staple. Sometimes there are a lot of people.

Parks to wander around near campus

Pet Care Resources

  • Sometimes you can get pet supplies at the APA thrift stores
  • Austin is very dog friendly and has many dog parks

Great web resources

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