New Announcements are Here.

Old ANNOUNCEMENTS:
see the Timeline and Timeline Vets pages for specific lab and assignment tasks


2015 Fall Stuff Below


Help us bring the holiday spirit to our TIDES office

create a decorative object using the materials in your lab or office.
The ornaments should fit in the display case outside the TIDES office
in order to be eligible for the prize, they should be submitted at the TIDES office by noon on December 9th.
Please attach the stream or group name to the submission in some way.
The winner will be chosen by vote by the FRI faculty and staff at the TIDES Staff Holiday party.
The winning group or stream will receive a pizza party, to be arranged by the supervisor.

How to Design a Research Poster: Workshop

Are you an undergraduate needing to learn how to design a research poster for a class or an upcoming conference? This Wednesday and Thursday, the Office of Undergraduate Research will be offering poster design workshops at FAC. Please sign up to attend. More workshops will be offered in the spring.

Wednesday, November 18 from 2:00 to 3:30 p.m. in FAC 330

Thursday, November 19 from 9:30 – 11 a.m. in FAC 332

Peter T. Flawn Academic Center (FAC) 2304 WHITIS AVE , Austin, Texas 78705

The Office of Undergraduate Research (OUR) offers workshops for UT undergraduates to support the creation and presentation of a research poster. Undergraduate students must register in advance for these workshops. The OUR is not able to support graduate students at this time.
The workshop emphasizes poster design principles; appropriate sections for a research poster; presenting your poster; understanding your audience; and evaluating a poster.





The Science Ambassador Scholarship is a full tuition scholarship for a woman seeking an undergraduate degree in science, engineering, or math, funded by Cards Against Humanity. The ideal candidate will be an ambassador for their field–someone passionate about discovery who shares their excitement with others.
http://www.scienceambassadorscholarship.org/


NSC is holding a graduate student panel this Wednesday, November 18th from 6:30 to 7:30 in NHB 1.720

to help undergraduates decide if graduate school is for them.
We will be having graduate students from the following departments:
-Chemistry
-Institute for Cell and Molecular Biology
-Physics
-Computer Science
-Neuroscience
-Pharmacy

As an undergraduate, I was always eager to get opportunities to talk to mentors about possible opportunities for career paths and know many students in FRI, especially VDS, who would be interested in this event. I would really appreciate it if you could tell your students about the event. They can RSVP using the following link to the Facebook event:
http://tinyurl.com/CNSgradstudentpanel
https://www.facebook.com/events/1036834826346955/



If you plan to present a poster at the Spring Undergraduate Research Forum. . .

The Office of Undergraduate Research (OUR) offers workshops for UT undergraduates to support the creation and presentation of a research poster in November, starting today. The workshop emphasizes poster design principles; appropriate sections for a research poster; presenting your poster; understanding your audience; and evaluating a poster. Students who attend poster design workshops will be added to the Office of Undergraduate Research Canvas site where they can access the workshop presentation and poster templates. If you are unable to attend a workshop and would like to request access, please email us your EID. You may also request an appointment for individual advising for poster design.
Fall 2015 Poster Workshops
Tuesday, November 3 from 3:30 – 4:45 p.m. in PCL Learning Lab 2
Wednesday, November 18 from 2 – 3:30 p.m. in FAC 330
Thursday, November 19 from 9:3011 a.m. in FAC 332
Sign up for a workshop



USE THE SUMMER TO TAKE YOUR RESEARCH EXPERIENCE TO THE NEXT LEVEL!

Join us at the CNS Summer Opportunities Workshop
Get the latest information on how to find, select, and apply for summer research and internship programs.
Learn how to craft a successful application. Get tips on writing the personal statement and fine-tuning your resume.

When:Friday, Nov. 6
Time: 3-5pm
Where: WEL 2.224
Box lunches will be provided! Prizes and giveaways!

To reserve your box lunch, RSVP to: http://bit.ly/1OQjD7s





2015 Texas Student Research Showdown Final Round
Support research by helping choose the six student finalists of the Texas Student Research Showdown. Currently enrolled UT undergraduates can submit the voting form only once, but can vote for as many of the 15 submitted short student research videos as they want.

The voting form will expire at 11:59pm on Wednesday, October 21, so vote now!

The 2015 Texas Student Research Showdown Final Round is scheduled for Thursday, Nov. 12, 2015 at 3:30-4:30 p.m. in the Avaya Auditorium (POB 2.302). The whole campus is invited to attend and watch the six finalists compete for $2500 in scholarships at this TED-talk style event. For more details, visit http://www.utexas.edu/ugs/our/showdown.





FRI Transitions Program

How do I continue to be involved in Research?
GOAL: facilitate the integration of undergraduate students into faculty research labs.
help you with the process of finding and joining a faculty lab.
PROCESS
find labs of interest to you ----- contact the lab ----- likely expectations of the lab ----- learn about possible credit ----- what to be ready for during the evaluation phase of joining a lab
These information sessions will be (identical sessions – not a two part series):
INFO Session 1 = OCT 27 at 4:30 in PAI 3.02
INFO Session 2 = OCT 28 at 4:00 in PHR 2.110
The Transition Program will also be available to help you on an individual basis at any step in the process thereafter.

Questions? Contact fritransitions@gmail.com


Bioscience and Biotechnology Career Fair (BABS) will be held on October 21, Wednesday at Texas Union Ballroom (UNB 3.202) from 1:00 to 5:00 PM. As of now 22 employers have signed up to attend this event (click here for the list of employers). Employers in attendance are seeking candidates for full-time, part-time and internship positions. Please visit the BABS career fair web site (http://www.engr.utexas.edu/ecac/183/6037-bioevent) for more information.

Antiparasite Drug Developers Win Nobel

TheScientist


“Genius” Grants Given

The MacArthur Foundation announces this year’s awardees.
TheScientistt

UT Austin Graduate School Fair - October 6th
Meet representatives from graduate programs across the country and around the world at the UT Austin Graduate School Fair, October 6 from 10am – 2pm in the Texas Union Ballroom. Over 60 programs will be in attendance, with more signing up every day.

Visit the Event Page for a full list of represented programs, and for more updates.

During the Grad Fair, there will be simultaneous panel discussions with UT faculty and with current grad students. The panels will talk about the benefits, challenges, and realities of graduate school, to help you decide if grad school is for you! Join us in the Santa Rita Suite from 10:30 - 11:30am or from 12:30 - 1:30pm.

Both events are free and open to all majors at UT. Click here to register.

Graduate School Fair
October 6
10:00am-2:00pm
Texas Union Ballroom


Is Grad School For Me?
October 6
10:30am-11:30am
12:30pm-1:30pm
Santa Rita Suite (Texas Union)
Faculty panel: Hear from faculty members in different areas who can tell you what they look for in successful applicants, how they select students, and the different kinds of funding available to students.
Student panel: Current graduate students can tell you what it is like to be a graduate student on the UT campus. They can also give tips on how to apply to graduate schools and what to expect when dealing with programs.


The Protein Society: Member Mini Grants
pic.jpg
The goal of this program is to enable members to hold protein science-reltaed events in their communities. These events could be meetings, seminars, workshops, experiments, networking or other small gatherings that bring groups together to learn, collaborate, share perspectives and make professional connections. Also encouraged are outreach events intended to communicate the unique appeal and fascinating potential of research involving proteins to junior investigators, students and under-represented minorities. Among members is VDSer Tony Garcia who sponsors an outreach program in the Austin area. For more information on this program go this the Protein Society's website below.

http://www.proteinsociety.org/join/benefits/minigrants/


Annual Biomedical Research Conference for minority Students

ABRCMS is one of the largest, professional conferences for underrepresented minority students, military veterans, and persons with disabilities to pursue advanced training in science, technology, engineering and mathematics (STEM). The conference is designed to encourage underrepresented minority students to pursue advanced training in STEM and provide faculty mentors and advisors with resources for facilitating students’ success. In 2014, VDSer Oscar Villarreal won a travel award to attend this prestigious conference! Paste this link into your browser for an in depth interview with Oscar conducted by ABRCMS officials.

http://abrcms.org/index.php/abrcms/abrcms-newsroom/35-2013/abrcms/254-interview-with-past-attendee-oscar-villarreal



Discussion with Sir Richard Roberts - Nobel Prize Winning Biochemist!
This An amazing opportunity for FRI student to hear a Nobel Laureate speak is approaching! UT-CSSB invites you to attend this discussion on the benefits of GMOs and Golden Rice in the fight to end world hunger. Don't miss it!

September 10th
1:00 to 2:00 pm
San Jacinto Hall, Room 207
For information email: ccervini@utexas.edu


Welcome back students! New Fall 2015 Research Conferences Update
Rice Conference.PNG

October 17: This fall the Gulf Coast Undergraduate Research Symposium, or GCURS, will be hosted in Houston, Texas at Rice University! Students can present research in a variety of fields, including: Biosciences, Chemistry, Computer Science, Statistics, and Electrical and Computer Engineering. However, if a student has another interest that may fit in one of these fields, they are welcome! The symposium is open to undergraduate students and their advisors. Students that are interested in pursuing a career in academia, or who are considering graduate study in these fields, would greatly benefit from the experience of presenting original research in their fields.

Please visit this website for further information: gcurs.rice.edu

Mol Bio Conference.PNG
October 17: This undergraduate research forum is for students to present the research that they have been conducting in an oral presentation. All biology and chemistry students are encouraged to submit abstracts! Selected abstracts will then be invited to present their research at the symposium. Abstract submission deadline is September 18 at 5 pm. Selected applicants will be emailed by October 1st.

Please visit this website for further information: https://sites.cns.utexas.edu/mbssg/fall-undergraduate-research-forum


Additional Conference resources:
Eastern Washington University - http://www.cur.org/ncur_2015/
Annual Biomedical Research Conference for Minority Students - http://www.abrcms.org/index.php/travel-awards

The 29th Annual Symposium of The Protein Society

July 22-25, 2015

Luis Valencia represented the Virtual Drug Screening stream of the University of Texas at Austin at the 3.5 day forum in Barcelona, Spain this past weekend. This event focuses on all aspects of protein science and is aimed at those scientists seeking to stay on top of the latest advances and developments. The meeting featured prestigious speakers, numerous workshops for educators and students alike and provided networking opportunities. Luis found this conference to be a great and humbling experience where he learned a lot and became interested in many new areas of biochemistry research. We would also like to congratulate Luis on receiving the award for Best Poster Abstract! He was one of two undergraduates to receive an award. You make VDS proud Luis!

For more information please visit the Protein Society Annual Meeting webpage here:
http://www.barcelocongresos.com.es/protein2015/welcome.html

nw5248_NikkiW_072715_LuisConferenceSpain1.PNGnw5248_NikkiW_072715_LuisConferenceSpain.PNG



What are we doing today?

see the Daily Schedule Summ15

==> Edit your Summer Student Schedules


Summer Researchers:

Mentors:
Andee F, Charina B, Nikki W.
Alberto
Super Researcher: Anita V., Tony G.


NAME-
Duration-

DNA Sequencing-
Transformation
Photo Release Form
Field Trip Release Form-
Field Trip Medical Authorization Form-
1
Jeff X.
June & July

red (forward)

yes
yes

2
Ashley C.
June & July

red (reverse)

yes
yes
yes
3
Bethany R.
June & July

green (forward)

yes
yes
yes
4
Ana R.
June & July

green (reverse)

yes
yes
yes
5
Steven T.
June & July

purple (forward)

yes
yes
yes
6
Kevin H.
June & July

purple (reverse)




7
Diane C.
June & July

red (forward)

yes
yes
yes
8
Elizabeth M.
June (part) & July






9
Anthony A.
June & July

green (forward)

yes
yes
yes
10
Matthew N.
June & July

green (reverse)

yes
yes
yes
11
Lisa S.
June & July

purple (forward)

yes
yes
yes
12
Simone M.
June & July

purple (reverse)

yes
yes
yes
13
Brittan M.

---
------




14
Priya M.

---
------




15
Kevin N.
June & July

red (forward)

yes
yes
yes
16
Krupa S.
June

red (reverse)

yes
yes
yes
17
Justin H.
June & July

green (forward)

yes
yes
yes
18
Mayur P.
June & July

green (reverse)

yes
yes
yes
19
Marisa S.
June
---





20
Hyuna (Hannah) K.
Summer Research Academy

red (reverse)




21
Arthi K.
Summer Research Academy

red (reverse)




22
Parker D.
June & July

red (forward)




23
Rachael B.
June and July
---
green (reverse)

yes
yes
yes
24
Sri N.

---





25
Matthew S.
June and July
---





26
Bella D
June and July

green (forward)























Schedules

please enter your summer class schedule here (if you are also taking classes in the summer or have other conflicts with lab work):
(Link TBD)

Mentor Schedules

Want to know when the mentors will be on? - check here (Link TBD)


Start Date: Friday June 5th -----------------------------------> End Date: ~ July 31st

Group Meeting/Journal Club

once a week
Location: GEA 100
Journal Club Wikispace Page
Group Meeting Slides are in the Google Drive folder

Spaces

PAI 2.14 wet lab
GEA 100
PAI 3.04H Dr. B's office
WEL 2.128 computer lab, WEL 2.144 computer lab
Painter 1st floor - ice room, autoclave, big centrifuge
Biotech lab - WEL 3.270
Robertus lab - WEL 5th floor
Chemistry Storeroom - WEL 1st floor (basement) - supplies and dry ice
Chemistry Electronics Shop - WEL 2nd floor (near computer lab)
BioScience Storeroom - NHB 1.502 - supplies
  • NHB glassware shop - next to BioSci storeroo
ICMB Core Facilities:
  • DNA Sequencing Facility (DASF) - MBB 1.426
  • ICMB Storeroom - MBB 1.426K (separate room for turning in invoice and for picking up items)
    • Can only pick up items from 9-12 AM and 2-5 PM


The Plan

We are going to work on our targets that we started picking in the Target Discovery Exercise.
First, we will review those and see if they are good.
Order overlap primers for our targets (we need these before we can start cloning for 'real')
While we wait on the primers, we will express, purify and characterize YopH & FtHap enzymes - 2 current VDS targets.
-- may also do NDM-1 and RpFabG

Then we will do some practice cloning procedures to teach you guys the new DNA cloning skills.
Then we will proceed to work on cloning our targets
Then we will express, purify and characterize our targets.
Then we will perform enzyme activity assays to see if our targets work
Then we will carry out inhibition assays


Lab Safety:

Have you complete your lab safety trainings?



Tours and Fun Stuff


  • Naturally Obsessed Form - when to watch this documentary- Please fill out this form....TBD

TACC Tour at VisLab in ACES building ON CAMPUS - @

    • (meet in lab before at to walk over)
    • Fill out - Medical Waiver
    • Fill out - Liability form

TACC Machine room Tour - @

    • (meet in lab before - then we'll catch bus up to Pickle campus)

GASF (Genome Sequencing and Analysis Facility) Tour in MBB 4.102 (not done)

    • Paper to read before the tour: NGS_Mardis.pdfAlgae Lab Tour: Meet in PAI 2.14 - then will walk over to BIO 320 (not done)


Skills List:

Target Discovery
PCR (primer overlap)
Restriction Enzyme Digest
Cloning
Plasmid Midi-Prep
DNA Sequencing
Protein Expression, Purification, Characterization (Large scale)
FPLC
Enzyme assays


Things to Keep in Mind

Wikispaces no like it when you have more than 3 windows open at a time! It be slow.
Store reagents at the proper temperature & in the right location (e.g. correct freezer box)
Label all reagents (tubes, boxes, liguids, powders) with VDS and Date (also include your initials if it is yours)
Write down everything that you do in lab into your lab notebook
Clean your area when done and return reagents and materials to their 'homes'

Aspire Awards Banquet


Tuesday, April 28, 2015


The College of Natural Sciences hosts the annual Aspire Banquet to honor the accomplishments of our top African-American and Hispanic students, both to celebrate their achievements and to inspire the continuation toward degrees and successful careers. In addition to students, college faculty, staff and alumni are invited to applaud student accomplishment. The banquet will include the presentation of awards and speeches by students and a distinguished guest. This event is a great opportunity for students to celebrate their success and develop mentor relationship with natural sciences alumni.

Congratulations to Xenia Gonzalez for her nomination and to Luis Valencia and Oscar Villarreal for their awards!

BOTH_BriannaLuisOscarDrB_Aspire.PNG


Success at the 2015 Undergraduate Research Forum

A big congratulations to VDSers Serena Zadoo and Antonio Garcia on their awards! Serena was awarded the CNS Award for Excellence in Biochemistry Research and Antonio the SURGe Award for Most Interesting Research Poster.
Visit this link for further info and full list of winners:
https://cns.utexas.edu/innovative-education/undergraduate-research/undergraduate-research-forum/awards-honors


Intellectual Entrepreneurship (IE) Citizen Scholars Hosts 4th Annual Research Contest

The Intellectual Entrepreneurship (IE) Citizen Scholars, IE's student organization, hosted its 4th Annual Research Contest for students from all disciplines on campus. The event was held on Monday, April 20, 2015 as part of the UT-Austin Research Week Events. The contest provides current and former IE Pre Grad interns and students interested in IE the opportunity to showcase their research, ambitions and aspirations. A total of 19 students were accepted to present their research; all were all eligible to win prizes. Several of UT's colleges and schools were represented: the College of Liberal Arts, the Moody College of Communication, the College of Fine Arts, the College of Education, the College of Natural Sciences, and the Jackson School of Geosciences.

Congratulations to VDSer Xenia Gonzalez for winning second place overall with her poster "Identifying a Novel Inhibitor for GES-5 Carbapenemase in Klebsiella Pneumoniae Infections by Virtual Drug Screening." Keep making VDS proud!


LONGHORN RUN

http://www.utlonghornrun.com/

Hmmm .... Science is hard.
http://www.theonion.com/articles/national-science-foundation-science-hard,1405/




For students that are interested to join the MBS club--this is a UT student affiliate of ASBMB. (American Society for Biochemistry & Molecular Biology)
meetings will take place in Welch 3.268 at 6pm this Wednesday (January 27th).
You can even RSVP to the meeting on the Facebook page
https://www.facebook.com/UTMolecularBS




Welcome to the VDS Stream!


Class Location and Time: BUR 216 on Tuesdays 3:30 - 4:30

Experiment Schedule and Due Dates for Assignments: Spring 2015




Buy a Lab Notebook:

  • Blueline notebooks (A9Q or A9, with or without grids, 192 pages costs $5.95) from the COOP
  • LabNotebookImage_outside.jpg LabNotebookImage_inside.jpgLabNotebookImage_insidepages.jpg



A note about turning In Assignments:

Title your filename appropriately – using the standard format that we have been using.
  • UTEID_Name_Date_AssignmentName.doc
  • Convert your document to a PDF


Spaces

PAI 2.14 wet lab
BUR - classroom
PAI 3.04H Dr. B's office
WEL 2.128 (and maybe WEL 2.144) computer lab
Painter 1st floor - ice room, autoclave, big centrifuge
Biotech lab - WEL 3.270
Robertus lab - WEL 5th floor
Chemistry Storeroom - WEL 1st floor (basement) - supplies and dry ice
Chemistry Electronics Shop - WEL 2nd floor (near computer lab)
BioScience Storeroom - NHB 1.502 - supplies
  • NHB glassware shop - next to BioSci storeroom
ICMB Core Facilities:
  • DNA Sequencing Facility (DASF) - MBB 1.426
  • ICMB Storeroom - MBB 1.426K (separate room for turning in invoice and for picking up items)
    • Can only pick up items from 9-12 AM and 2-5 PM


Things to Keep in Mind

Wikispaces does not like it when you have more than 3 windows open at a time! It be slow.
Store reagents at the proper temperature & in the right location (e.g. correct freezer box)
Label all reagents (tubes, boxes, liguids, powders) with VDS and Date (also include your initials if it is yours)
Write down everything that you do in lab into your lab notebook
Clean your area when done and return reagents and materials to their 'homes'



+++++++++++++++++++++++++++++++++++++++

Science Olympiad

March 28th, 2015

Protein Modeling Event

40 points - prebuild
30 points - onsite build
30 points - exam

LINK TO THE BUILD ENVIRONMENT
Pre-Build FOK1 2fok.pdb.
__http://cbm.msoe.edu/scienceOlympiad/designEnvironment/prebuild.html__

OnSite Build Model
__http://cbm.msoe.edu/scienceOlympiad/designEnvironment/regional.html__


CHANGES!
We will use 1.5 cm per residue (NOT the 2 cm per residue as prescribed)

You will only receive 4 feet (~122 cm) of toober which is enough for only about 81 residues
- so, we will remove residues #1, #83 and #84 from the model.
- use residues 2-82
+++++++++++++++++++++++++++++++++++++++



Spring 2015
Undergraduate Research Forum VDS Poster
Here is the poster that you guys will be presenting at the forum this Friday. Make sure you take a look at it and you are familiar with the content, if not please ask Oscar or Melissa about it.



2014 Fall Stuff below



iGEM
Interested in synthetic biology - cloning, etc.?
http://igem.org/Main_Page
iGem info session Wednesday Dec. 10th, 5 pm in WEL 2.122


ABRCMS! San Antonio

Oscar V. and Vicky G. presented their work
Oscar brings home some hardware (or rather paperware and money)!
ABRCMS2014_VDS (5).jpg







Rice - Gulf Coast Undergraduate Research Symposium

http://gcurs.rice.edu/
Oscar V. and Vicky G. presented their work as 10-12 minute oral presentations. Aptamer stream also sent several students and Neuroscience of Synapses, Functional Materials, Bioprospecting, Synthesis and Biological Recognition.
Vicky was awarded the prize for the best presentation in her section. Congrats Vicky! And thank you to both for representing the FRI (and VDS well).

Karthik R. (a VDS alum) represented UT in the Electrical Engineering talks.

Joey O. (now at Rice as a grad student) served as a Judge (I am sure he was completely unbiased!)











FALL 2014

Split class Rosters .... see the Schedule Fall 14 (semester)



What are we doing today?

see the TIMELINE

Schedules

please enter your class schedule here ( or other conflicts with lab work):
LINK HERE

Mentor Schedules

Want to know when the mentors will be on? - check here Google Calendar
Mentor Conflict sheet

Start Date:Wed August 27th



Group Meeting/Journal Club

once a week
Location: ????
LINK TO JOURNAL CLUB
Group Meeting Slides are in the Google Drive folder

Researcher's Names:
  • Summer Veterans: Andee, Brianna, Carolyn, Charina, Chris T., Cidia, Luis, Nikki,
    • Partial Summer: Andrei
  • Sidestreamers: Hailey, Zain (both full summer)
  • Springers:
  • Course Conflict people:

Spaces

PAI 2.14 wet lab
GEA - classroom
PAI 3.04H Dr. B's office
WEL 2.128 computer lab
Painter 1st floor - ice room, autoclave, big centrifuge
Biotech lab - WEL 3.270
Robertus lab - WEL 5th floor
Chemistry Storeroom - WEL 1st floor (basement) - supplies and dry ice
Chemistry Electronics Shop - WEL 2nd floor (near computer lab)
BioScience Storeroom - NHB 1.502 - supplies
  • NHB glassware shop - next to BioSci storeroo
ICMB Core Facilities:
  • DNA Sequencing Facility (DASF) - MBB 1.426
  • ICMB Storeroom - MBB 1.426K (separate room for turning in invoice and for picking up items)
    • Can only pick up items from 9-12 AM and 2-5 PM

The Plan

For Veterans
- continue cloning target and move towards protein work and virtual work.

For Returning Springers
Picking targets in the Target Discovery Exercise.
- First, we will review those and see if they are good.
Order overlap primers for our targets (we need these before we can start cloning for 'real')
Then we will do some practice cloning procedures to teach you guys the new DNA cloning skills.
Then we will proceed to work on cloning our targets
Then we will express, purify and characterize our targets.
Then we will perform enzyme activity assays to see if our targets work
Then we will carry out inhibition assays


Lab Safety:

Have you complete your lab safety trainings?

Skills List:

Target Discovery
PCR (primer overlap)
Restriction Enzyme Digest
Cloning
Plasmid Midi-Prep
DNA Sequencing
Protein Expression, Purification, Characterization (Large scale)
FPLC
Enzyme assays



Things to Keep in Mind

Wikispaces no like it when you have more than 3 windows open at a time! It be slow.
Store reagents at the proper temperature & in the right location (e.g. correct freezer box)
Label all reagents (tubes, boxes, liguids, powders) with VDS and Date (also include your initials if it is yours)
Write down everything that you do in lab into your lab notebook
Clean your area when done and return reagents and materials to their 'homes'




Class Time Scheduling
Please fill out the class scheduling forms for the times that work for you:

Part 1: https://docs.google.com/forms/d/1QXiIVK4efVxCHaKvlgosK-nOJYKtlxCnkhOCCpCMS0M/viewform?usp=send_form#start=invite

Part 2: https://docs.google.com/forms/d/1uBMzocbdgZ01iD4rFRXP6xz2npo0uaXHVZjAJA5VKbE/viewform?usp=send_form#start=invite




SUMMER 2014

see Summer14

2014 Undergraduate Research Forum Posters for VDS



2014 Summer, 2014 Spring, and 2013 Fall Stuff Below:


BOWLING on THursday July 23rd at 6:00-7:30 pm in the Union!
see Summer14


Movie Social

Hey VDSers!
It's been a while since we've had a social. Since our stream works with infectious diseases, I thought that going to see Contagion on April 6thwould be a great social! The movie is free on campus and starts at 6. We'll probably head over at 5:30 just to make sure we can get seats together. If you're interested in going, please reply! You can just show up, but it would be nice to get an estimate of how many people are going!
-Priya
=)

WIRED SuperBug:

Serious Resistant Infections Increasingly Found in Children

http://www.wired.com/wiredscience/2014/03/serious-resistant-infections-increasingly-found-children/

Summer Fellowship Applications:

Due March 25th

http://www.cns.utexas.edu/fri/beyond-the-freshman-lab/fellowships

Also - if you are interested in volunteering only (don't need the cash) - then talk with Dr. B





Secrets of Managing with a Heart - talk on Tuesday

Tuesday, March 25, 2014, 05:15pm
http://cns.utexas.edu/new-content/manage-events/icalrepeat.detail/2014/03/25/412/-/managing-with-a-heart
John Paul DeJoria, philanthropist and co-founder of Paul Mitchell and The Patrón Spirits Company, will be giving a talk for students on the importance of connecting with people first and foremost as we manage our careers and lives. DeJoria, a member of the College of Natural Sciences Advisory Council, founded JP's Peace, Love and Happiness Foundation in 2011 to invest in charities that share the core values of his companies -- sustainability, social responsibility and animal-friendliness.


GOLD STAR WINNERS!

Congratulations to the following VDSers, for having the top notebooks! Keep up the excellent work.
PyMol2 & Buffer Titration
Charina B
Andee F
Saniya H
Ariana L
Alberto T
Carlo (Gio) O
Tyler S
Luis V
Avery W
Sanjna Z





GOLD STAR WINNERS!

Congratulations to the following VDSers, for having the top notebooks! Keep up the excellent work.
Buffers and Solutions:
Andrei L.
Andrea F.
Anh P.
Stacy T.
Nikki W.
Kennan W.
PyMol 1 and Beer's Law Labs:
Andrei L.
Alberto T.
Nikki W.
Avery W.
Kennan W.

To all of you other awesome VDSers, we saw some really good notebooks. Make sure that you keep up with the good points, and take into account our suggested improvements. Remember, developing the skill of writing a fantastic lab notebook will be a lifesaver when you need to look back and reference it later on down the road. And remember, Joey and all of the mentors are always available to talk to you about specific concerns regarding notebooks.


Create an account for Wikispaces: (for the Mini Research Wiki Assignment)

  • Use your first name and last initial for the login. e.g. joshb
    • If you have the same first name and last initial as someone else - then the next letter in your last name e.g. joshbe


Experiment Schedule and Due Dates for Assignments: Spring 2014










LONGHORN RUN

Do you run? Do you walk? If so, you should do the Longhorn Run this year with TeamFRI and represent your favorite program!! Sign up by February 7th and get 20% off registration fees when you use the "EARLYBIRD" (ALL CAPS) code. The race is on Saturday, April 12th at 8:00 AM and it starts/finishes outside Gregory Gym.

To register with Team FRI:
1) Go to this link: https://www.edsregistration.com/events/64

2) Choose a distance; 2 mile or 10K
3) Enter “FRI” in the line that says "List 1 student organization you are affiliated with"
4) Use the code “EARLYBIRD” (case sensitive) for 20% off race fees
Follow the event on FB for team updates and announcements.



If you have any questions, please contact Eman Ghanem: eghanem3@gmail.com. Invite your family and friends to join TeamFRI today!


The race is sponsored by the UT Student Government and Recreational Sports. Proceeds go to the UT Student Government's Student Excellence Fund.



This is a web site for first generation college students funded by the Gates Foundation.
http://www.imfirst.org/stories/

Welcome to the VDS Stream!


Class Location and Time: BUR 216 on Tuesdays 3:30 - 4:30


Things to start working on by the first week of class:


Read the Syllabus:
  • see link on left hand side menu 'Syllabus'

Lab Safety Training:

  • Start completing your online lab safety training: see link on left hand side menu 'Required Lab Safety'

  • Lab Safety Walk Throughs for this 1st Week (Meet in Lab PAI 2.14). Sign Up Sheet
    • (NOTE: this also has sign up for the non-mandatory Help Sessions for Literature Search Assignment)

Lab Scheduling

  • Please fill out this: 'SchedulingVDSClassforGDocsSpring14forGDocs' - see the Canvas page for this link
  • Voluntary Buffers and Solution Sign-Up
    • Early sign ups for Part 1 of Lab 1 on Friday Jan 14th
    • MLK Day Sign Ups for Main Part of Lab 1 (if you can't make MLK day, we will schedule you at other times throughout the week)
      • you will need to have already done the Lab Safety Walk Throughs

Buy a Lab Notebook:

  • Blueline notebooks (A9Q or A9, with or without grids, 192 pages costs $5.95) from the COOP
  • LabNotebookImage_outside.jpg LabNotebookImage_inside.jpgLabNotebookImage_insidepages.jpg







A note about turning In Assignments:


Title your filename appropriately – using the standard format that we have been using.

  • UTEID_Name_Date_AssignmentName.doc

  • Convert your document to a PDF

Upload to the DropitTome site. This is a write-to only directory. So, you won’t be able to see anyone else’s files that have been dropped there.

LINK to Upload Site: http://www.dropitto.me/vdsclass


Upload Passwerd: same as our GDocs

2013 Spring and Fall Stuff Below:



The Natural Science Council is hosting a FREE lunch for students accompanying their favorite TA or student mentor on 11/1/13. Students must nominate their favorite TA/mentor & RSVP for the event by 10/30/13; email nsc.sf.chair@gmail.com to RSVP. More information about the event may be found here, http://tinyurl.com/student-ta-lunch2013



FRI Rotation Program:

http://fri.cns.utexas.edu/rotation
help place former FRI students in Faculty labs. It has been more focused on the biology and biochem labs. The student and Faculty member will work out the expectation (hours, time and possibility of credit).
Spring 2014 Applications are available. Please apply by November 28, 2013
https://www.surveymonkey.com/s/HSNX3LH


PBS Show on Hunting the Nightmare Bacteria (Tuesday night)
Frontline
http://www.pbs.org/wgbh/pages/frontline/pressroom/press-release-hunting-the-nightmare-bacteria/

Of interest:
CDC Select Agents List
http://www.selectagents.gov/Select%20Agents%20and%20Toxins%20List.html



Be cool and get the mobile App for ICM for your iPhone (iTrash) or Android.

http://www.molsoft.com/iMolview.html


COOL TALK:
The Rise of Neglected Tropical Diseases and Poverty in Developing
Countries and the Southern United States with Dr. Peter Hotez
Tuesday, October 1, 2013
5:45 PM - networking time
Actual talk starts at 6:30 pm
Location: AT&T Executive Education and Conference Center Amphitheater (Room 204)

REGISTER: http://bit.ly/14nfYau



HHMI Janelia Undergraduate Program - Neuroscience research in summer (very good program)
http://www.janelia.org/student-programs/undergraduate-program

Superbugs = bad
http://www.wired.com/wiredscience/2013/09/cdc-amr-rpt1/

ACS (American Chemical Society) Southwest Regional Meeting - Waco, TX Nov. 16-19th, 2013
http://swrm.org/overview-69th-swrm/undergraduate-program/

Rice Regional Undergraduate Research Symposium - Sat. October 26, 2013
http://biochem.rice.edu/RUS.aspx

Senate of College Councils Undergraduate Research Grant
http://utsenate.org/urg/

Undergraduate Research Fellowship (Utexas)
http://www.utexas.edu/research/resources/awards-fellowships-grants





090313
We officially have the coolest classroom on campus now! - GEA 125 (old library in Gearing Hall)
-- we will start meeting there tomorrow for both the Early Class & Late Class
http://www.utexas.edu/maps/main/buildings/gea.html





HPC Penguin Video
http://www.youtube.com/watch?v=TGSRvV9u32M



7/22/13
IDT T-shirt Pic

IDT_B_FRI_Utexas.jpg


7/1/13 - Pics of VDSers are in the Google Docs/Pics folder




What is 'publication bias'?
http://f1000.com/resources/Negative_Results_PR_WEB.pdf


VDS Paper in the Stanford Undergraduate Research Journal (on the page, search for 'virtual')

http://www.stanford.edu/group/journal/cgi-bin/wordpress/?page_id=373

FRI Ambassador Program (get paid to visit your high school and talk about FRI)

FB page for the program. interested students can post their questions there https://www.facebook.com/FriAmbassadorProgramUtAustin?ref=hl


VS4 Protocol posted. See the NDM-1 Beta-lactamase Project page

End of Semester Bowling Party (At the Union)

Friday (May 3rd) at 3 pm - a great opportunity to wear funny shoes and embarrass yourself on the lanes!

Responses to form:
https://docs.google.com/forms/d/1FP7iOgw5wE8Yn_9sU62PJjaA-pB6iVeRpNPUjtEyxUQ/viewanalytics


SummerResearchFormVDS_2013

Fill this out if you are interested (or not interested in summer research)
https://docs.google.com/forms/d/1lB_xT7y7c-R0m5DKy08ItI3I0tJB-0qD6cfxw1-_mgQ/viewform#start=invite

Summer Housing Form

https://docs.google.com/forms/d/1_7Usr45BeZAtAFZPUSAOUF5XLVnbTNkSjo5_8-k4NIo/viewform

VDS T-shirt is available for purchase for $14 through TxShop.

-- You can use your credit card or UT account.
We have 31 orders now - we need a total of 40 to make the purchase! (as of April 18th)


VDSers win Forum Awards!

Life Technologies Award for Excellence in Biochemistry Research ($500)

Kaarthik Rajendran

SURGe Students’ Choice Award Honorable Mention ($50)
Vanna Hovanky



Registration Info for Fall 2013 VDS Class

Fall 2013
BIO 377 UNDERGRADUATE RESEARCH-FRI 51325 W 2:00 - 3:00 BUR 108
OR
CH 369K TECHNIQUES OF RESEARCH-FRI 53170 W 2:00 - 3:00 BUR 108

Answers to some course credit questions for Fall:

Chemistry and Biochemistry Majors
CH 369K counts automatically in Chemistry and Biochemistry degree plans. Students in Chemistry or Biochemistry are required to take six hours of upper-division CH beyond the degree requirements, including three hours of lab credit. CH 369K counts as the three hours of lab.
Biology Majors
All BIO options except for Neurobiology and Microbiology are supposed to count BIO 377 automatically. Neurobiology majors can count BIO 377 by petition once the credit is earned.
Micro majors can petition to count BIO 377 before they take the credit (I’ll be submitting a request for blanket approval of this credit).
Public Health Majors
The PBH degree plan does not have a large lab requirement, so neither BIO 377 nor CH 369K counts for any specific requirement. The only required labs are the general CH lab (CH 204) and a microbiology lab (BIO 226L). The FRI credits will just work as upper-division hours for the degree.



ASSIGNMENT DUE DATES: (updated 4/22/13)

Due Date: (@ midnight unless stated otherwise)
Assignment Name:
Wednesday (Feb 13)
Lab Report for Beer’s Law
Monday (Feb 18th)
Wiki Post for Mini-Research Write Up
Saturday (Feb 23rd) @ 5 pm
Lab Notebook Due (PyMol2 & Buffer Titration)
Monday (Feb 25th)
Peer Review Assignment (for Beer's Law Report)
Saturday Mar 1st
Wiki Voting for Mini-Research Post
Monday (Mar 4th) Thursday (Mar 7th)
Final Beer's Law Lab Report (submit as PDF not DOCX)
Saturday (or when done with last step) (Mar 9th) @ 9 pm
Lab Notebook Due (PyMol3 & Protein Expression)
Mon 25th
Summer Fellowship Applications




Mon (3/25) changed to Thursday Mar 28th @ midnight
changed to Sunday Mar 31st @ midnight
Lab Report: Virtual Screening 1
Sat (April 13th) @ 5pm
Lab Notebook due (VS2 & Protein Characterization)
Mon (April 15th) @ mn
Changed to Wed (April 17th) @ mn
Lab Report (Online): Protein Labs Combined
Wed May 1st @ 7 pm
Lab Cleanup - your samples


by Wed May 1st @ m/n
Lab Notebook due (VS3 & Target Discovery & VS4)
T.B.D.
Lab Safety Quiz on BB







Journal Club Article for 14th Class

(print out and bring to class)
ParkStructureBasedVirtualScreen_PTP1B_EuJMedChem2009.pdf

Pre-class Questions
(answer and bring to class)
13VDS_13thfor14thClassJournalClubQuestions_PreClass.docx


Longhorn Run Results:

http://www.mychiptime.com/searchevent.php?id=7453%20

LonghornRun_2013-04-13.jpg

LonghornRun2__2013-04-13.jpg





















Monday, April 15th
Panel as part of Research Week - the importance of doing undergraduate research as it applies to obtaining work (both industry and academic) after graduation. The event is open to students of any major.
The scheduled panelists are:
Dr. Gregory Daniel Frank, Ph.D., Director of Business Development, XBiotech
Dr. Jeanette Hill, Ph.D., Founder and CEO, Spot on Sciences
Nichole Wiedemann, Associate Dean for Undergraduate Programs (UT School of Architecture), Associate Professor
Dr. Barbara Brown Wilson, Director, Center for Sustainable Development (UT School of Architecture), Associate Professor

Research Panel Flyer_PDF.pdf



Longhorn Run

Packet Pickup
in Gregory Gym Thursday, Friday
  1. see the FB event page for other info
  2. Since the FRI logo is on the back of the shirts, Dr. Ghamen has FRI stickers and ribbons to be placed on the shirts, race bibs, or wherever you wish! This way, team members are easily recognized. These items may be picked up from her office (WEL 5.424) - on a table outside.
  3. Pre-race FRI team members picture is on Saturday, April 13th at 7:30 AM on the steps outside PAI on 24th st. Please be there on time; the speedsters would want to line up early at the start line!
If you have any questions, please email eghanem3@gmail.com. See you all on Sat! Go Team FRI!



Forum Poster Times for Friday

- see this spreadsheet for your assigned time to 'man' (or 'woman') the poster
(Tip: use 'Ctrl+F' to find your name)
https://docs.google.com/spreadsheet/pub?key=0AvGl3lMyhDsodE9hNlN2QUFlTVBjdUpuT0xvcXNWRkE&output=html








Cool PDB Poster on 'How Drugs Work'

poster








Poster Names for Forum Poster Author List
see:
PosterNames


VDSer wins big (again)!

Vanna won the 1st Place Grand Prize in Life Science, the major category encompassing all of the projects in the categories of: Animal Science, Behavioral & Social Sciences, Biochemistry, Cellular & Molecular Biology, Environmental Management, Medicine & Health, Microbiology, Environmental Science, Plant Science.
statefair1.jpeg


Online Lab Report for Protein Labs moved 2 days later.

See Table below.

Labs: VS2 & Protein Characterization

- you have 2 weeks to complete both of these. You don't have to finish VS2 before starting Protein Characterization
- it is recommended to sign up for one of the early Protein Characterization time this 1st week if you can.





033013 - if you want to read ahead - the VS2 assignment is posted to BlackBoard

VS1 Lab Report

- now due on Sunday March 31st at midnight.

Stumped on your lab report? -------> see the F.A.Q.'s

( VS1 Lab Report Question and Answers )
http://vdsstream.wikispaces.com/VS1+Lab+Report+Q%27s+and+Notes+Sp13

The Virtual Screening 1 Lab Notebook will be due NEXT Saturday 3/30/13 with the Protein Purification Lab Notebook as well.
Pre-Lab Q's for Virtual Screening 1
https://docs.google.com/forms/d/14iiSXJrW58-GylZY2YQqAsCUGd662t8bVko-8lRk2d0/viewform





































Extra VS1 help session

WEDNESDAY from 5- 8 pm in Welch Computer Lab


10th Class 'Live' Quiz form and results

FORM


RESULTS








WIRED news article on Antibiotic resistance
http://www.wired.com/wiredscience/2013/03/cre-cdc/



Longhorn Run:

There's a new promotion code for the 10K part of the Longhorn Run on April 13th . Use the code RUNTHEWORLD (case sensitive) for $5 off registration fee. Details on how to join Team FRI and all team updates are on the FB event page. Please share with your students. Let me know if you have any questions.

College of Natural Sciences Summer Research Fellowships (FRI summer research)
http://cns.utexas.edu/honors/scholarships-fellowships/current-students/research-fellowshipsNOTE: you can apply to receive a paid fellowship - but you are also welcome to do research as a volunteer if you can be present for a significant part of the summer (1-2 months) - (just talk to Dr. B)

LabNotebookD Grade statistics:

AVG
9.30
MAX
10.00
MIN
7.10
STDEV
1.29
MEDIAN
9.7

GradesLabNotebookD_Py3ProExpressSp13.jpg

GOLD STAR AWARDS for Lab Note D (Py3 and Pro Expression)

ARIEL
AARON
ASHLEE
ADITI
BRENDAN
FENG (Fin)
GRACE
JACQUELINE (Jacky)
JAMES
KHADY
KATHERINE (Renee)
KEELY
MARIANNA
Madeline
SHIVANI
SERENA


GradesLabReportBeersLaw_ScreenShotSp13.JPG


Mid Semester Meetings with Dr B





Mini Research Wiki Contest Prize Winner:

MiniResPrizeCertificateSp13.JPG








SCHEDULES:

ScheduleVirtualScreening1_Sp13

SchedulePyMol3_Sp13
ScheduleProteinExpression_Sp13
ScheduleBufferTitration_Sp13
SchedulePyMol2_Sp13


















FINAL Beer's Law Lab Report

Can be submitted as a PDF (instead of as a .DOCX as it says in the handout)

Class Pics
Next week (Tuesday March 5th) we will take our class picture - either before or after class


Extra PyMol Sessions:

Saturday (3/1) all day in Painter 2.14 Wet Lab (use VDS laptops or bring your own)

Monday (3/4) from 6-8 in Welch Computer Lab --- Daniel is the mentor

Tuesday (3/5) from 6-8 in Welch Computer Lab - mentor is TBD

Peer Review Assignment posted:
http://vdsstream.wikispaces.com/PeerReviewSp13

FORM for Report Extension Request & Extra PyMol Sessions

https://docs.google.com/forms/d/1q2R0FZ4YRgKEda1FG4WinJ9A105D0w5Fqh4j8HqM7H0/viewform

Lab Notebooks (022812):
Class Average: 9.13 STDEV: +/- 1.68 Max grade: 10 Lowest Non-zero: 7.60 Median grade: 9.4

GOLD STAR AWARDS:
Congratulations to:
Grace T.
Caroline
Aditi
Young
Katherine V.
Gautiam
Jacqueline E



Also, Lab Pics that we have taken of you can be found in the GoogleDrive/Pics folder (when you go to that folder, you have to click on the 'gridview' button on the right to see the images)

VDSer wins big!

Vanna won 1st place in Microbiology in the Science Fair. She also received Best of Fair, giving her the opportunity to participate
in Intel's International Science and Engineering Fair at Phoenix, Arizona.

DSC_8667.jpg


Cool Poster of PROTEINS from the PDB that was shown in class:

PDBposter_Reduced.pdf

H-H Equation Help:

http://www.ccunix.ccu.edu.tw/~deptche/02.pdf



VDS T-shirt is available for purchase for $14 through TxShop.

-- You can use your credit card or UT account.

Confirmed T-shirt orders as of 0201213
Alyssa J Kahl
Ms. Melissa Huynh
Michael Tra
J Gomez


Aaron J Hong
Janice Kim
Ramiro P Rodriguez
Shelby D Fisher- Garibay
Daniel T Obrien
Nicolet J Finger
Emily E Johnson


Mr. Grant D Tippet
S L Wolf
Mr. Kaarthik Rajendran
Jiaqi Zhang



Ariel Chen
lhrlogo12colorlla.jpeg
==

==



Longhorn Run

FRI Runners!

Team members are invited to Victory @ Gregory Gym on
Thursday 2/14 at 5:30 PM for the official announcement of the winner of the
Student Organizations Competition. There is also a 'grub run'
scheduled at 6 pm and team members are invited to run and to enjoy some food
afterwards. Additionally, Nike would like to allow members of Team FRI to test
some new footwear. They would be allowed to 'check out' the footwear for
the run at 6pm. Please note that all team updates are being posted on the
FBevent page If you would like to receive team updates and announcements via
email, please send an email to Eman Ghanem: eghanem3@gmail.com.
Thanks everyone!

Join Team FRI:

The team that registers most runners by Feb 13th wins customized race day t-shirts.
1) Go to this link: http://www.edsregistration.com/races/256/registrations/new?team_id=1023

The race is on Saturday, April 13th at 8:00 AM. To register with Team FRI:
2) Choose a distance; 2 mile or 10K
3) Enter “FRI” in the line that says “Please List 1 student organization you are affiliated with”.
4) Use the “STUDORG” code for $5 off,
------ NOTE: the code is case sensitive




VDSers - a reminder to take pictures of your lab notebook if you would like to have the information in it for your Lab Report since the notebooks can't leave the lab.































Beer's Law Lab Handout posted to BlackBoard


Schedule (Beer's Law) - in wet Lab

----- NOTE A: Saturday lab times are available. If you start on Saturday - your Lab Notebook is not due until Monday (Feb 11th) for Beer's Law.
---- NOTE B: 2nd Monday lab times are available. If you start on the following Monday (Feb 11th) - your Lab Notebook is not due until Tuesday night (Feb 12 th) for Beer's Law.
--- NOTE C: Lab Report for Beer's Law Postponed until Wednesday (Feb 13th) at Midnight for All







Lab Notebooks:
Class Average: 8.49STDEV: +/- 0.71Max grade: 9.70Lowest Non-zero: 6.2Median grade: 8.6

GOLD STAR awards:We also had 4 gold star awards for exemplary notebooks! Congratulations to:Serena ZKavya KYoung L.Ashlee W

Schedule (PyMol1) - in Computer Lab











Help Sessions: Excel Setup & Analysis

We will be having a Help Session: Excel Spreadsheet & Graph for Part 1 Location: WET LAB location PAI 2.14 (posted on Wikispaces schedule)THURSDAY: 4:30 - 6 pmFRIDAY: 3:30 - 5 pm

With what you have now - you can analyze Precision. However, you need to add some more to analyze Accuracy.This Help Session will allow you to make sure you have your spreadsheet setup & that you are able to analyze it properly.It is a drop-in session. So, you can come in anytime it is open. Also - it is not mandatory - especially if you have already had Dr. B check your spreadsheet.

Flu Shots Today (Wed): - go get one!

DATE: Wednesday, January 23, 2013
TIME: 9am – 2pm (or while supplies last)
LOCATION: Student Services Building Glenn Maloney Room (SSB G1.310)
(This is a “walk-in” clinic – appointments are not available).


Mini-Research Write Up selection Form is posted

- see link on the left hand side menu

Lab Safety

Due by class on Tuesday (or before you start lab if you are doing Monday lab)
Bring a printed copy to class or put directly in our lab safety section of the sign-in binder in lab
You can check what we have down for you so far:
http://vdsstream.wikispaces.com/Required+Lab+Safety

Lab This Week:

- BE SURE TO SCROLL DOWN on the Spreadsheet if you don't see your name!






















FALL 2012 Stuff Below:


Link to form
https://docs.google.com/spreadsheet/viewform?formkey=dFVLNFJFYXMyOEpaWDBsUHhYNTBKLVE6MQ
Results to form


Writing Help Sessions

-- need help with writing your final report? Come ask Dr. B some questions.
Location: PAI 2.14 Wet Lab (if we have enough people, we will migrate to a classroom)
THURSDAY: 3:30-5:00
FRIDAY: 3:30-5:00


T. brucei (African sleeping sickness) and cool Laser X-ray crystal structure procedure
http://phys.org/news/2012-11-x-ray-laser-sickness-exploiting-parasite.html

Class Picture!
In class on Wednesday (12/5) - around 75% of the way through class ~ 2:45




Final Report Guidelines (due Sat Dec 8th)
VDSFall12_GuideFinalReportonTarget_VDS_Fall12.doc

CIS (Course Instructor Surveys)

VDSers - don't forget to fill out the CIS forms online. We won't do a paper version this semester.
CH 369K (52275)
https://utdirect.utexas.edu/ctl/ecis/





We are going to test a new upload method for Assignments.

I would like you to use this tonight for your M&M_ExpressionPurification
Title your filename appropriately – using the standard format that we have been using.
UTEID_Name_Date_AssignmentName.doc
Convert your document to a PDF
Upload to the DropitTome site. This is a write-to only directory. So, you won’t be able to see anyone else’s files that have been dropped there.
LINK to Upload Site:
http://www.dropitto.me/vdsclass
Upload Passwerd: same as our GDocs


11/25/12 -
M&M for Expression Purification Characterization: see ......
Virtual M&M due - Tuesday at Midnight.
see VDSFall12_Guide_M&M_ExpressionPurification_VDS.docx in Google Docs


11/26/12
A reminder about the FRI Rotation program - if you are interested in continuing research in another lab.
http://fri.cns.utexas.edu/rotation



By popular vote: Class will be on:
Monday Nov. 19th 5-6 pm in RLM 12.166 (two floors up from the other class room)

CLASS DATE CHANGE NEXT WEEK:
https://docs.google.com/spreadsheet/viewform?formkey=dHJPb3oxVklDSkhDQ01NMkVCXzdqbWc6MQ

Lab Hours this weekend: Saturday and Sunday

PyMol Image Contest voting is up

Reminder - lab notebook check this weekend. Due on Friday (unless you work on Saturday - then it is due Saturday)

M&M for Virtual Screening: see ......
Virtual M&M due - Sunday at 9 pm.
see VDSFall12_Guide_M&M_Virtual_VDS.docx in Google Docs


LabHoursWk10withAvg.JPG




111212 -
We are getting the ISO numbers from each of you to get you access to the ICE/AUTOCLAVE/CENTRIFUGE room.
We have a card swiper and a WORD document set up on one of the laptops in the lab for you to enter (swipe) your ISO number along with your UTEID - please see the Mentors if you have a question about it.



NCUR Conference in April
http://www.cur.org/ncur_2013/



1. due date for applying to be a mentor for Spring 2013 VDS is coming up on Friday Nov. 9th. Everyone is encouraged to apply. If you have any specific questions about mentoring - please come talk to me or send an email.
There is a 1 day lag between when you post your resume/create an account and when you can actually apply to the job. So, try to do this by Thursday Nov. 8th!

http://fri.cns.utexas.edu/beyond-freshman-lab/peer-mentoring-program


2. The due date for the M&M for Cloning is being pushed back to Thursday night. This way you will be able to take a look at my comments on your Research Reports first.
Guidelines for M&M Cloning (also posted to GDocs in /Results&Data/M&MCloning/)
VDSFall12_Guide_M&M_cloning_VDS.docx


110512 -
Undergraduate Research Journal (URJ) at UT-Austin.
The goal of the Undergraduate Research Journal is to promote undergraduate research on campus and publish the highest quality articles. This is a great opportunity for undergraduate students to share their excellent work with the academic community. If you are interested in submitting your project (as a team probably) to the journal, the link to the URJ website is: http://texasurj.com/




The author of the winning article will receive a $200 prize, and the second-place winner will receive a $100 prize.
The deadline for submission is 11:59 p.m. on February 22, 2013.


110512 - VDSers - clean up your station after you work in the lab. If you repeatedly don't cleanup - it will affect your final grade! Do not expect the Mentors to clean up after you. Good researchers always leave a clean lab.

NOTE: spectrophotometers should not be left ON for extended periods of time - the lamps will burn out - just like a light bulb at home.











103112 - Christina will be mentoring in lab this Saturday (11/3) (and maybe Joey too?)

102312 - This is a reminder that the Undergraduate Research Grant application is due November 2 - for Senate of College Councils

101612
Attend - the FRI Informal discussion about graduate school on Thursday, October 25, from 5-6pm in WEL 3.502 (the James Harvey Shell Auditorium, entrance on Inner Campus Drive).
Panelists with PhDs in the Chemical and Biological sciences.
Graduate School Panel Flyer.docx

Target Group Meetings

we will have meetings of each target group with Dr. B sometime this week or next.
We'll discuss where you are and where you should be in the next few weeks and how to work as a team/partners on the projects.
It should take about 20-30 minutes. We'll meet in Dr. B's office.

102212 - Christina will be mentoring in lab this Saturday (10/27) (and maybe Joey too?)

FRI ambassadors - spreading the word of FRI

Ambassadors are current FRI students and mentors who wish to visit their high school over winter break to share their FRI experience
with their former teachers and students.
-- check it: http://fri.cns.utexas.edu/beyond-freshman-lab/fri-ambassador-program

Each ambassador will be awarded $50 stipend for gas in addition to a polo shirt.
2 info sessions: Thursday, November 1st 7-8 pm & Thursday, November 8th 7-8 pm. Both are in WEL 2.256
You dont' have to attend the session to join - just contact Dr. Ghanem (Research Educator): eghanemATmail.utexas.edu

More details included in the attached flyer.
FRI Ambassador Flyer-FA12.pdf



Attention all Pre-Meds (or those that will have heart disease later in life...): you are encouraged to attend this FREE seminar on the UT Campus:
http://www.austinforum.org/
Thursday, November 8th at 6:30 pm in the AT&T Conference center
Dr. B is out of town - but just show up and sign in. Business casual attire is good. Jeans and nice shirt is probably acceptable (no black tie..)


FRI External Open House - Wednesday 10/24 1 - 4 pm.
VDSers - when you are in lab, clean up the area around you so that the lab looks professional for our visitors. -- Thanks,
Dr. B


LabHoursWk7withAvg.JPG



Nurses-at-bedside-1959-300x201.jpg

See One, Do One, Teach One

Training for the Big Centrifuge and Autoclave. Each person must get 3 'check offs' in order to use the machine on your own.
At the front counter of the lab, there is a Sign Off sheet. For each training session you do, fill out your info and get a signature.
Use the protocol posted online for the Big Centrifuge.(Beckman Centrifuge Protocol.docx)

At least one of your training sessions must be supervised by Dr. B. The other ones can be supervised by a mentor or Dr. B




101812 - Christina will be mentoring in lab this Saturday. Note: it is a UT home football game though (at 7:00) so it may be hard to get on campus.

101812
Note about Research Reports on Target
Put more effort into the Introduction with the background info. The Proposed Methods section does not have to have a ton of detail. Since these are proposed methods - you will talk about each protocol or step but you wouldn't put so much detail into it as you would find on a Published Research paper.
For example, you don't necessarily need to say what concentration of dNTP's you would use in your PCR - but you should address what type of PCR you are doing and generally how it works (e.g. Overlap PCR assembles oligos into a full length CDS which is codon optimized,... etc.). In a Published Paper methods section - you would list details like the concentration of dNTP's because, ideally, another researcher should be able to replicate your work using the information you have given.






101512
NOTE: the new version of GOLD (ver. 5.1) uses a new scoring system (PLP). The values of scores is different than what you would have gotten back in the Spring with GOLD Fitness score.
http://beta-www.ccdc.cam.ac.uk/Lists/DocumentationList/gold_release_notes.pdf

GOLD_5dot1_ReleaseNotesScreenshot.JPG


NOTE: for the concatenation scripts - use the ones in the /home/chem204/scripts folder instead of the one that is in the VirtualScreenRefresherFiles
-- these will allow you to append your Bestranking.lst and Output.sdf files correctly.



100812 -
Virtual Screening Protocols are posted (these are for your real target - not practice)
in GDOCS /Protocols/VirtualScreeningProtocols/
ProtocolHomologyModelVDS_v3.doc
ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
Protocol_ICM_VDSv1_3.docx

Decide if you need to do a homology model first.

Also - we will screening some with ICM this semester.



100312 -
GuidelinesResearchReportonTarget_VDS_Fall12.doc
Also, Journal Club StudyQ's and article posted under Journal Club page


092812 - Springers and Sidestreamers - PyMol refresher due date changed again to this Sunday Sept 30th - i would rather you focus on your
---- ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc
092612 - Springers and Sidestreamers - PyMol refresher due date changed to this Saturday Sept 29th
092612 - Springers, be sure to upload your Midi-prep concentrations of pNIC-Bsa4 Midi-prep to Google Docs /Misc/PlasmidConcentraions

LabHoursWk3withAvg.JPG

Journal Club tomorrow - print out paper and also answer the Study Q's

Springers - since you have completed most of the practice work - you should start coming in on your own time (when a mentor is present) to get your project moving forward. IF you aren't sure what the next step is - ask a Mentor or Dr. B.

VDSers - in order to make it easier to comply with the long pants rule for lab - we have bought some scrub pants (dark blue) for you to wear. They are stored over by our lab notebooks by the window. -- Thanks, Dr. B

Article on Inha (FabI or FabV) inhibitors in Mycobacterium tuberculosis
http://the-scientist.com/2012/09/19/beating-drug-resistant-tb/


Are you signed up for the Undergraduate Research UT email List? - If not, sign up here:
https://utlists.utexas.edu/sympa/info/undergrad-research

Like animals & science? - check out this VMD-Ph.D. program
http://research.vet.upenn.edu/Default.aspx?alias=research.vet.upenn.edu/pennvetphd


LabHoursWk2.JPG


091112 - URF - Undergraduate Research Fellowships - for Spring term research (mentors and current VDSers can apply)
http://www.utexas.edu/sites/default/files/files/URF_2012-13_Guide.pdf
WHY
  1. get $ to buy supplies for your research project
  2. looks good on a resume


091012 - NEW classroom: RLM 10.176

LabHoursWk1_5.JPG



Interesting article:
http://phys.org/news/2012-08-method-production-proteins-drugs.html


9/20/12 -- Andy Ellington's Game Changers talk at 6pm on 9/20 at KLRU in Studio 6A (CMB 6th floor) (http://www.utexas.edu/gamechangers). Andy Ellington's talk is titled "Do I Really Need a Doctor for That? Technology Should Allow Us to Diagnose Ourselves."


090612
Analyze DNA Sequence for Springers will be 3:30 ~ 6:30 on Friday Sept 7th in WEL 2.114


090612
New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik
---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx
You can use either Q5 or KOD polymerase. But we are out of KOD right now!

090512
Time for a new classroom! Since we were evicted (so rudely) from our last group meeting - we will seek out another location.
This will most likely be Burdine 108 unless I can get access to another room. -- Dr. B

PS - be sure to check the GroupMeetingSlides on Google Docs for the slides we weren't able to cover.

Download the Journal Club paper and the Study Questions. The study questions are due at the beginning of next class.













  1. Welcome back! We will be meeting Wed 2-3 pm in RLM 11. 176 (not the burdine location listed on clips). This a better classroom for our journal club since it has moveable desks.
  2. For people returning from the Spring (i.e. not summer folks) we will have a Target Discovery Session in WEL 2.114
  • immediately after class.
  • the next day (Thursday 1- 5 pm)
If you can - plan to make the first meeting - we will be picking our new drug targets and we want to get this process done as soon as possible. We would like to order our primers by Friday.












END SPRING - SUMMER 2012 ANNOUNCEMENTS



Mushroom talk:
http://www.ted.com/talks/paul_stamets_on_6_ways_mushrooms_can_save_the_world.html


AUGUST 22nd 7 PM- "Carbon Nanotechnology" Lecture by Dr. James Tour at the AT&T Conference Center

Info: http://us2.campaign-archive1.com/?u=3ceb27481539d3ea886b7b2bb&id=bebc805130&e=89bb926b3d

Register: https://ricemba.wufoo.com/forms/ra-austin-chapter-distinguished-professor-event/

Wear Business Casual Attire


Hours072012_c.JPG

072612 - Thursday 3:00 - GASF (Genome Sequencing and Analysis Facility) Tour in MBB 4.102

Paper to read before the tour: NGS_Mardis.pdf






NOTE - not change in schedule

TACC Tour at VisLab in ACES building ON CAMPUS - @3:00 Wednesday 7/11

(meet in lab before at 2:50to walk over)




Snippet from one of our Spring VDSers:
http://www.flickr.com/photos/utcns/7069737591/in/set-72157629248580161/

Monday 7/2
Fourth Summer Group Meeting 2:30 in Welch classroom
Tuesday 7/3
3:00 - Algae Lab Tour: Meet in PAI 2.14 - then will walk over to BIO 320

Naturally Obsessed viewing
Meet at the lab at 5:30 to head over to Dr. B's house
Will use cars or can also take the #21 Bus that leaves from Dean Keeton & University @ 5:47 pm
The Naturally Obsessed viewing will be Thursday June 28th form 6-7 pm at Dr. B's House

Naturally Obsessed Form 2 - when to watch this documentary- Please [[#|fill out]] this form.... for the SECOND time!

https://docs.google.com/spreadsheet/viewform?formkey=dHp6M2hkcE16RlRLcW1wcHNPTXp3Vmc6MA


Naturally Obsessed Form - when to watch this documentary- Please fill out this form....
https://docs.google.com/spreadsheet/viewform?formkey=dGdJaEQ5cUtEQm1uaXJ5LVNNdUR4NkE6MQ


See the Daily Schedule ......

Sixth Summer Group Meeting

Fifth Summer Group Meeting - Monday

Fourth Summer Group Meeting - Monday

Third Summer Group Meeting - Monday June 11th at 2:30

Second Summer Group Meeting - Monday June 4th at 2:30


First Summer Group Meeting

We are planning to have our first meeting on Thursday 5/31 (next week) at 1:00 in PAI 2.14. (Except the new highschoolers - won't come until June 11th)

Summer Scheduling

I want to get an idea of when people will be available to be in the lab. So, I have created a Google Docs spreadsheet that I would like each of you to help fill in.
Go to the link and find your column - then input the times that you have class or you know you have some other commitment.

https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodHdWY3lTNGFRaUxLVk9kRE9iaFllTXc




High School Researchers - start date:
Session 1: Monday, 6/11/2012 - Friday, 7/6/2012 Session 2: Monday, 7/16/2012- Friday, 8/10/2012



Vanna & Keyur win big!

They competed in Intel's International Science and Engineering Fair (ISEF). The project won a Second Place award from the American Association of Pharmaceutical Scientists and a Fourth Place Grand Award in Medicine and Health Sciences.
ISEF_Photo.jpeg





AAPS_Award.JPG











https://docs.google.com/spreadsheet/viewform?formkey=dGdSWlExeDJYUDl6a2Rfc1BBMlVRNnc6MQ





Fill out [[#|survey]] for VDS Social!

Clean Up days: ....


Be sure to check the Google Docs - Pics folder for pictures form the Forum.

Virtual Screening help for VS3 lab this week will be in the Wet Lab (you can use the [[#|laptops]] in PAI 2.14)

Virtual Tip: If you're gold_cat script doesn't work, type this to make it a unix file:
$dos2unix gold_cat

04/19/12 - The Notebooks and Final Report for VS3 and the Enzyme Lab are not due until Thurs. May 3rd

041812

Wolbachia Assignment

(Sort of like the PseudoKnot assignment)
As a class, we need to see if these Wolbachia targets have similarity to known PDB structures. This will count as a mini assignment and is due on Monday (April 30th) at Midnight.
Wolbachia Targets

Lab Enzyme Assay Sign Ups (starts this Friday!)

https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodEFuMXo5M1VOczJuUHM2UXBQTVU3RGc



041812

Fall Class Credit Clarification:

For BIO majors if you take the fall VDS class:
-- the BIO377 credit counts as upper division bio lab for most majors.
-- the CH 369K - counts as upper division elective credit (need 36 upper division hours)

For BIOCHEM majors
-- the BIO377 credit counts towards a required 9 hours of coursework from Natural Sciences, Engineering, and Geology outside of CHEM
-- the CH 369K - counts as Lab credit and Upper division credit (so, this would be the obvious choice for BIOCHEM majors)

Also, if you plan to take Organic lab sometime - you will need to have the CHEM204 credit. So, if you did not take VDS for the CHEM204 credit this Spring - you may want to take the regular CHEM204 in the FALL to get that out of the way.


041812 - A reminder to answer the VDS_13thfor14thClassJournalClubQuestions_PreClass.docx on the Journal Article and bring your answers to class on a sheet of paper to turn in.
We will also work in small groups to do a mini - Journal Club

041712- Journal Paper to read and discuss (with Quiz?) in class in about ~ 3 weeks (April 24th class - 14th class)
ParkStructureBasedVirtualScreen_PTP1B_EuJMedChem2009.pdf











04/15/12 - Class this week will be in WEL 2.144 computer lab (3:30-4:30)
Sign Ups for VS3 lab
VS3signupscreenshot_notfilled.JPG

Also - a reminder to post your Favorite Posters from the forum to the Wiki spaces


Reminder

Online lab reports for Protein Labs are due Monday night (April 16th)
-- use the Protein Labs link to the left











Undergraduate Research Forum - Friday April 13th

http://cns.utexas.edu/research/undergraduate-opportunities/undergraduate-research-forum
[[#|Sign Up]] for Presentation Times
Choose your favorite poster on the Favorite Posters page


Poster Time for Undergraduate Research Forum
Spring 2012 -

Use this Google Form to select your 3 best times:
https://docs.google.com/spreadsheet/viewform?formkey=dGltT2NTcGJRTUNqck90V3FKWmhzTnc6MQ#gid=0

Be sure to sign in on sheet and take one of the slips of paper to write down your Favorite Posters from Forum. Then copy that information to the Wiki page.


'Friday the 13th' ....... scary.....
11-11:20
Michael
Ramya
Sajan
11:20-11:40
Daniel
Fiona
Amron
11:40-12:00
Suman
Kevan
Mihir
12:00-12:20
Janice
Shreya
Drew
12:20-12:40
Ruifei
Alex
Divya
12:40-1:00
Tom
Jihye
James
1:00-1:20
Stephanie
Kaarthik
Aldo
1:20-1:40
Andrew
Ling

1:40-2:00
Inez
Zamaria

2:00-2:20
Urvashi
Brandon
Shashika
2:20-2:40
Max
Shane
Cody
2:40-3:00
Zachary
Landon


Aakash - variable (also presenting his own research)

Copy of This Year's poster (take a look so that you know what will be on it for the Forum):


Disease Detective Conference - Monday & Tuesday April 9th, 10th

April 9th Monday:
6:00 pm – 7:00 pm: SCIENCE STUDY BREAK
SAC (1.402)
In conjunction with the conference Dr. Richard Taylor (Biology) will discuss public health and infectious disease topic, using scenes from the movies 12 Monkeys and Contagion, and the TV shows "The Walking Dead" and "Numb3rs".
http://www.lib.utexas.edu/lsl/StudyBreak/SSB.html

April 10th - Tuesday
CONFERENCE - free lunch at Noon
5:00 - Instead of VDS class on Tuesday everyone is expected to attend the 5:00 Keynote Session in SAC 1.402 - Check in with Dr. B when you get there
http://www.sbs.utexas.edu/diseasedetective/default.htm

Disease-Detective-2012-Program.JPG








040512 - for VS2 lab, when finding Lipinksi's data on MTX and FOL - search on Pubchem website for those two.

NCUR Conference Pics

https://docs.google.com/open?id=0B4O2KqKh2q_-MjhjZjQ4NjktYmRhNS00ZTczLWIzNDEtY2I0OTVjZWU1MWRl
HINT: next to the search box - in the pull down list - select 'IMAGES' to see the pictures.

Sign-Ups for Next Week's Lab (Protein Characterization Gel)

https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodExnV3Rva1VVU1NVNms3ZXd1Z214X0E
- Note the Gel Drying step must done at least a day after running the gel. You must come in during one of the assigned gel drying times only for this step (but you don't have to sign up for it - just come by).


04/03/12 - VS2 lab notebook not due for 2 weeks (due at same time as Protein Characterization Gel lab notebook)
---------------- Both due on Saturday April 14th at 5:00 pm - if lab is closed - put in desk drawer in hallway for Adam to grade.

04/02/12 - Class will be in WEL 2.144 (computer lab) this week.

Sign Ups for VS2 - This lab does not have a report and the lab notebook won't be due for 2 weeks.
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodF9wUFBtSGtUSnp1a2JQSXBUSmxfcFE








Protein Purification Labs Sign Ups

Go to this link to enter your selection.
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodEdXS1JkSWhaM2Z4Q0VYejNBSVltREE
ProteinLabsSignUpscreenshot.JPG

032212 - see note below about TEJAS award.

Mid-semester Meetings

Please sign up for a time to meet with Dr. B this week. This is a chance for use to catch up and allow me to get to know you better in a one-on-one setting without being in the middle of a lab.
https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodG1KN1FCYV82MGtoOEk5SWpFRXlZMkE

031512 - FRI RUN


Join TEAM FRI! The FRI will be taking part in the Longhorn Run this April 14th. Come join us and get some mileage into your legs.

You are encouraged to RSVP on the Facebook page for team updates and also to get an idea of how many are joining the team.
This is open to everyone; not only students.
https://www.facebook.com/events/271792789566677/

Team members receive $5 off registration fees. This brings the 10K fees down to $25 and the 2mile fees to $20. The promotion code to join the team and get the discount is LHRFRI, which is good until April 5th.







03/10/2012

We're halfway through the semester and there's only a few labs left, Congrats VDSers! Finished grading your notebooks and they looked pretty sweet! -- Have a relaxing and enjoyable Spring Break, you guys definitely deserve it after all the hard work you guys put into those notebooks.
-Adam


TEJAS Awards

The Texas Excellence in Jobs and Service Award [[#|application]] is posted on UT Direct. This is an opportunity for current Spring 2012 FRI students to be offered an hourly stipend for doing research in the Fall 2012 as opposed to credit. It is a merit-based and need-based offer. Please contact Dr. B if you have any questions about your eligibility. Basically this is an award for students who want to continue doing research but may not normally be able to because of a part time job that would limit their time. The award offers a stipend to offset a portion of the financial aid package that would otherwise require loans. The average award is $1500-1800 for 10-12 hrs of research per week.
- applications due CHANGED TO March 27th (a Tuesday)
https://utdirect.utexas.edu/scholarship/student/menu.WBX?s_scholarship_owner=E&s_scholarship_ccyys=&s_user_role=S
NOTE: need to have a complete FAFSA in order to be eligible for the Tejas awards.


FRI Summer Research Fellowships

The summer is an optional opportunity to advance your research. (You can skip it and still come back for the Fall class)
However, those that take part in the summer experience (either paid or as a volunteer) will gain skills in genetic cloning and expression of their drug target, enjoy a fun and small-group based atmosphere, and engage in a more in depth approach to research where you don't have to worry about classes and tests!
- applications due March 23rd (a Friday)
http://cns.utexas.edu/honors-scholarships/scholarships-fellowships/research-fellowships


20 Questions & Voting for Mini Research Wiki

Due Date: Thursday March 8th @ Midnight Friday March 9th @ Midnight


030506 - Class Picture tomorrow class!
Some pics have been added to the Google Docs. You have to click on the Pics folder and then from the Drop Down menu at the top, select 'Images' to see them as pictures instead of file names.
GoogleDocs_ImagesViewingInstructions.png

FRI Summer Research Fellowships

- applications due March 23rd (a Friday)
http://cns.utexas.edu/honors-scholarships/scholarships-fellowships/research-fellowships

Protein Expression Lab Scheduling:

SERIES W:



Started Last week
Michael, Brandon

2nd Step Mon AM
All

3rd Step Mon PM:
All

4th Step Tues PM:
All



SERIES A:



Thursday Start: ,
Zamaria, Sajan,

Monday Start:
Inez, Shane, , Max, Amron, Kevan (orB), Shashika, Cody, Zach

2nd Step Tues AM:
All

3rd Step Tues PM:
All

4th Step Wed PM:
All



SERIES B :



Friday Start:
Ruifei, Fiona, Suman, Ivy, Jihye, Tom

Tuesday Start:
Alex, Drew, Ramya (orD), Aldo, Shreya (orE), Landon

2nd Step Wed AM:
All

3rd Step Wed PM
All

4th Step Thurs PM:
All




SERIES C:



Wed Start:
Divya, Ling, Aakash

2nd Step Thurs AM:
All

3rd Step Thurs PM:
All

4th Step Fri PM:
All



SERIES D (Skip a day):



Mon Start:
Urvashi, Janice, Karthik

2nd Step Wed AM:
All

3rd Step Wed PM:
All

4th Step Thurs PM:
All



SERIES E (Skip a day):



Tues Start:
Stephanie, Daniel, Andrew (was A), James (was B)

2nd Step Thurs AM:
All

3rd Step Thurs PM:
All

4th Step Fri PM:
All








Fri Mar 2nd - Pseudoknot Due, MiniResearch Wiki Assign Due, Lab Notebook due at 7:00.





Monday Feb 27th @ 4 - 5 pm: Lab Report Writing HELP SESSION - with Dr. B and mentors in WEL 2.114
Friday Feb 24th @ 4 - 5 pm: Lab Report Writing HELP SESSION - with Dr. B and mentors in PAI 2.14
-- note: these will also be help sessions for anything else (MiniResearch Wiki Assign, Henderson-Hasselbalch Exercise, Pseudoknot project Assign....)


022112 - Due Date change for MiniResearch Wiki Assign - now due Friday March 2nd at Midnight
022112 - Pseudoknot Project Assignment also due Friday March 2nd at Midnight

022112 - no lab notebook due this week (Buffer Titration) - but Lab Report due on Monday (2/27) at Midnight
022112 - Henderson-Hasselbalch 12VDS_6thClass_Exercise.docx due on Tuesday (2/28) in class as a paper copy (or scan and email to dr. b)

Cool showing various proteins' shapes and sizes


F.A.Q.s about first lab report:

Q: Do I need to show calculations in the lab report?
A: You do not need calculations in lab that are just routine calculations. You probably should show really important equations (like A=Ebc) and C1V1=C2V2. But you don't need to show all the calcs that you did.

Q: What images do I need in the report?
A: You need the spectra (from Logger Pro) of your single wavelength read that you got the Max Absorbance from. (right click and copy and paste it into WORD). You need your Excel table. You need your Excel graph with your BestFit line. Note - your graph should show your standard curve AND your unknown data point on it.





LabNotebooks for Report

020812 - VDSers - be aware that your lab notebook needs to stay in the lab. If you need your data and results to write your report - you will need to save a copy electronically or you can scan pages of your notebook using the scanner in the lab (white thing over by the printer). You can also take a picture of your notebook pages with your phone.
You probably don't have the LoggerPro software on your computer - so be sure to transfer the data to Excel so you can open it later and access your final graph that you made.



020612 - Lab Report due next Monday on Beer's Law
020612 - Lab notebook is not due this week but it is due Friday (2/17) - it should contain BOTH Beer's Law and PyMol2

020112 - Article on FRI in the Scientist by Dr. Sarah Simmons

020112 - If you want to 'like' the FRI facebook page, follow this link.
https://www.facebook.com/pages/Freshman-Research-Initiative-The-University-of-Texas-at-Austin/226650510716683

01/29/12 - REMINDER: Class will be in WEL 2.144 computer lab (3:30-4:30). Right afterwards we will start the Lab for PyMol1 in the same room.

01/28/12 - Hey VDSers, congrats on finishing your first wet lab! Just wanted to say you guys did very well on your notebooks. Keep it up so you can make my job easier, and we wont have any problems ;) See you kiddos soon. -Adam



01/25/12 - Lab Notebooks should stay in the lab. There is a cabinet for VDS notebooks near the window where you can write your name on a slot and keep your lab notebook. You can write in them anytime the lab is open - but they should stay in the lab.

01/19/12 - Lab 1 Scheduling is posted. See the Google Calendar link to the left.

T-shirts for VDS

–Cost ~ $18/shirt
–Follow link on TxShop for pre-order
170410_UT_Natural_SciLC2.jpg

170410_UT_Natural_SciB.jpg

011712 - NOTE

the WELCH computer lab has been moved. The correct number is WEL 2.128 or 2.144 (just around the corner from each other)
The 1st and 2nd Help Sessions (Wednesday & Thursday) will be moved to the Wet Lab (PAI 2.14)

To [[#|register]] for the Wikispaces page -
  • Use your first name and last initial for the login. e.g. williamb

Welcome new VDSers!

ExperimentSchedule_Spring12_Screenshot.JPG

1st Week Items:

  • Lab Safety Training (in person, online) DUE: Mon Jan 23rd
    • see 'Required Safety Training' link in the menu to the left
    • help session this week (and next monday)

- DUE: Mon Jan 23rd

Complete the CURE pre-survey of research skills (10-15 minutes)







BEGIN SPRING - SUMMER 2012 ANNOUNCEMENTS






Final Plasmids

For those of you that were successful in your cloning, you will need to get a sample of your good plasmid to Dr. B for future use in the VDS stream.
there is a 'Final Plasmids' box in the -20degC upright freezer. Place your sample in there.
The tubemust be well labeled so that we know what it is (Initials, Date, species initials, plasmid name, concentration - e.g.JTB 11/28/11 Yp YopH pNICBsa4 1.6 lambda - is 1.6 ug/ul)
If you have not Midi-prepped your plasmid, talk to Dr. B. We can have the mentors do this step. We need either mini-prep DNA or a colony of DH5alpha to get started.
FtHap in pNIC-Bsa4 - Christina, Joey
YopH in pNIC-Bsa4 - J.C.
SalCA in pNIC-Bsa4 - Krishna
MPTPB in pNIC-Bsa4 - Joshua
PSTP in pNIC-Bsa4 - Sadhana
PP2C in pNIC-Bsa4 - Justin
SfApy in pUC19 - Indra


Final Lab report due time posted - see Timeline pages




11/21/11

Vary Substrate Assay Protocol for Carbonic Anhydrase is posted to Google Docs

The Inhibition Assay Protocol for the Phosphatases is posted to Google Docs



11/17/11 - Compounds are in!

For those of you working on MptpB, YopH, FrTuHP, and PSTP - your virtually screened compounds from Chembridge are in.
So, once you have done the Enzyme assay and the Vary Substrate Assay, you can work on the Enzyme Inhibition Assays with these to get your final graphs.


See Protein Expression tips & hints for modifications to protocol





HOURS

LabHoursWeek11.jpg
Fig. 1. VDS class Lab Hours. Average is for semester-to-date. Week 11 (11/7 – 11/11)



Research Presentation Schedule:

Research
Technique
Aug 30th
none
none
Sept 6th:
Krishna, Sadhana
DNA sequencing/Analyze DNA sequence: Joey
RE digest and Nanodrop: Marshall
Sept 13th

PCR and Overlap PCR: Justin
- include Codon Optimization
Gel electrophoresis (mainly for DNA but also protein): J.C.
Sept 20th
Indra,
Larry
pNIC-Bsa4 LIC cloning: Joshua
Sept 27th
Journal Club
Midiprep/Miniprep: Sadhana
Oct. 4th
Marshall, Justin
Transformation, Expression - bacterial growth: Larry
Oct. 11th
Journal Club
Purification: Krishna
Characterization: Indra
Oct. 18th
J.C., Joshua
Enzyme Assay: Hong
Oct. 25th
Journal Club,Chijiioke, Jericho

Nov. 1st
Joey, Michael,, Hong

Nov. 8th
Journal Club,Ronnie,Mohammed,
Johnny

Nov. 15th
Shreya, T.J.,Giancarlo,

Nov. 22nd
Shutian

Journal Club 6

Nov. 29th

Presentations of Final Results (InhibitionAssay Graphs)
Instructions: prepare 5-10 Powerpoint slides to present your work to date
You must meet with Dr. B to review your presentation by the Friday before you are scheduled to present.
Upload your presentation before class to the GroupMeetingSlides folder on Google Docs
  • Intro (talk about your disease and what your protein does), Objectives, Methods& Results, Future Directions
Guidelines:
  • prepare a 10 minute powerpoint slide show
  • Start out with a title slide that has the Title and Your Name on it
  • Create an introduction that provides a broad perspective for the disease being presented. Then provide some background on the protein and what it does.
  • Talk about the methods you used - why did you do certain steps?
  • Talk about any mistakes or failures that would help other in the class.
  • Make an effort to explain what is going on in the figures
    • Include a caption
    • You can also make your own cartoons and schematic diagrams or show relevant pictures
  • Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
  • Talk about your immediate next steps
  • Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
  • Go through your talk at least once as a practice run



NOTE (as of 07/19/11): use new grant account number for DNA Sequencing jobs (it is already on the form for you in a pull-down list)- otherwise get it from Dr. B or Thao.

Saturday Hours:

This Saturday, Thao (11/???) will be in lab starting at 2-4 pm if you want to work.
If you don't need any help - you can come in earlier - since the lab will be open starting around 9 or 10 - with an Aptamer mentor.

Undergraduate Research Journal

Submission Due date: Feb 17th. URJ Call for Papers.pdf
ACS meeting scheduling
On Google Docs

11/04 - Journal Club Paper and Study Q's are posted for next week.

Protein Expression Scheduling:

Here's the Sign Up Form on Google - new guys and returning Spring VDSers should fill this out by Monday night.

Availability for Protein Expression:

Ronnie - Wed, Thurs or Fri of Next Week
Mohammed - Thurs (10/3) of Next Week
Shreya - Thurs (10/3) of Next Week - or Sat
Jericho - Tues (11/1) (maybe), or Thurs (11/3) of Next Week, or Fri or Maybe Sat
Johnny - Friday (11/4) of Next Week
Shutian - Fri or Sat
Giancarlo
Chijioke - next week (need YopH clone first)
T.J.


Last WEEK:

Thursday Oct 25th
Friday Oct 26th
Saturday Oct 27th
1
Michael E.


2



3
T.J.


4



Undergraduate Research Grant

URG_Application_Fall-20111.doc

External Open House Scheduling

The open house is planned for next Wednesday (Nov. 2). Each student will be available in the lab for a 30 minute block of time (1 hour block for summer stipend recipients) to interface with visitors about VDS stream and your specific project. You should update your Wikispaces page and have your PyMol image ready.

Here are the assigned times: (Note this is Version 2 - changed 10/25/11)

ExternalOpenHouseVDSClassScheduling.jpg


Voting Form on Google Docs - for PyMol Image Contest

https://docs.google.com/spreadsheet/viewform?formkey=dGRRUGJ1MGJDYVRQaERWN3ZOMXhSUlE6MQ

Virtual Screening Help Sessions:

Tuesday Oct. 25th, after class: 5-6:30
ProtocolVirtualScreenTopLigands_VDS_Fall11.doc has been posted

New Virtual Screening Tip (Wed 10/18)

see Tips & Hints page

Virtual Screening Help Sessions:

Monday Oct. 17th, 4- 5:30
Tuesday Oct. 18th, after class: 5-6:30
PyMol Image contest Due Friday at Midnight

Research Report

for those of you that have been averaging 10 hrs or more in the lab, you have an extension on the Due Date for the Research Report to Friday Oct. 15th
  • Sadhana, Joshua, Justin, Joey, Krishna, Indra

Virtual Screening Help Session

  • Tuesday after class in WEL 2.306 Computer Lab.
Also help on Research Report write up.

Virtual Screening Help Session

for those of you having trouble getting your Virtual jobs set up for YOUR target, there will be a help session:
  • Monday 4 - 5:30 in WEL 2.306 Computer Lab.
You need to have a library started by Tuesday night and having done this will help give you some content for your Research Report write up.

PyMOL refresher

please move (or better yet - copy) your PyMolRefresher Assignment to the /Results&Data/PyMolRefresher folder in GoogleDocs so that I can grade them

Virtual Refresher

do the same thing


Lab Safety Check:

  • check the Lab Safety page for your record of training. This will be part of a grade for next week.
EXROP summer research fellowships through HHMI (Howard Hughes Medical Institute) - talk to Dr. B if interested.

Virtual Screening Lesson - How to use SSH and GOLD.

  • Thursday 5 - 6:30 Welch computer lab
  • the New VDSers: Shreya, Hong, Marshall, Indra, Joshua
  • For older VDSers - you can use this as a help session if you haven't done yours Virtual Screening yet.


Help Sessions: PyMol and Virtual Screen Refresher in Welch Computer Lab
  • Thursday Sept 15th: 4 -6 pm
  • Monday Sept 19th: 5-7 pm
Science Works Assignment: create a profile. Here is a document10.pdf
ScienceWorksBanner1.png






Natural Sciences Career Expo
Monday Sept. 19th at the Frank Erwin Center
Don't forget to get your 'bling' on DressingDosDontsCareerDesignCenter.pdf

PyMol

we will tentatively be having a PyMol help or both new and old VDSers
  • Monday 5- 7 pm in WEL 2.306


Interesting article on antibiotic resistance.
1st Part of the Last 2 Labs: Virtual Screening 3 protocol:
2nd Part of the Last 2 Labs: Enzyme Inhibition Assay handout: and protocol:
The Pre-class Questions for the Journal Paper discussion on Tuesday can be found here.
PTP1b virtual screening paper: Read before the last 2 labs.


  • We will be doing the Protein Characterization Lab for next week. We will work in pairs as much as possible.
    There are 2 days to the lab
    Day 1 (long): prepare samples and run gel and stain gel
    Destain overnight
    Day 2: Image destained gel (30 min)


    Dry gel on dryer and take another image (2 hrs)

    We have 6 spots open on Monday afternoon starting at 3:00 if you would like to get the lab started early.
    For the gel drying - we will have several Drying Times. You can come to any of these to dry your gel (we just need to use the machine in groups at set times)


    Handout:
    SDS-Page Manual:




  • Handout: NOTE: the first version of this had the WRONG due date. This is now changed - it is April 11th Monday.

    See the Forum Presentation Times for your assigned time

    Sign up sheet for Poster Session at the Undergraduate Research Forum Friday April 8th

    Handout: [[file/view/LabProteinPurificationVDS_Spring11.docx|LabProteinPurificationVDS_Spring11.docx]]

  • PTP1b virtual screening paper: Read before the last 2 labs. [[file/view/ParkStructureBasedVirtualScreen_PTP1B_EuJMedChem2009.pdf|ParkStructureBasedVirtualScreen_PTP1B_EuJMedChem2009.pdf]]

    **Next Step Central** ( Assignment due Tues March 22nd)
    Summer FRI Fellowships Application (Application date: Tues March 22nd


  • Reminder: in addition to your lab notebook on Friday - you will need to post the images from your lab this week (Protein Expression) onto your page in the Protein Labs section of the Wiki.

  • change of lab for next week. No Virtual Screening -- Wet Lab instead. Fill out Scheduling FORM here
  • Pymol 3 and Buffer Titration notebooks are due Saturday at 5 p.m. If the lab is locked, you can leave your notebooks in the desk in the hallway.
  • Each student should sign up for a time to meet with Dr. B. Use the link below (we will meet in Dr. B's office Painter 3.04H). Mid Semester Meetings Sign Up Sheet for Week of March 1st - 4th
  • Lab Reports for PyMol 2 are graded. If you would like to pick them up - come by Dr. B's office (or I can give it to you at our one-on-one meetings)

Scheduling for Protein Expression Wet Lab (Week of Mar. 7 - 11th)



ScheduleForProteinExpressionLab_SeriesA-E.JPG

SeriesA: Mon > Tues > Wed
SeriesB: Tues > Wed > Thurs
SeriesC: Wed > Thur > Fri
SeriesD: Mon-------Wed > Thurs
SeriesE: Tues------Thurs > Fri
Unknown

Somto
Krishna
Sadhana
Ronnie
T. J.


Chijioke
Ar'Niqua
Jeanette

Luke
Saurabh

Johnny E
Christina
Mohammed

John N.
Joey

Mark
Juan S


Larry


Lindsay
Jericho





Michael E
Esther





Giancarlo
Shutian





Tyler
Nicole






Justin