Old+ANNOUNCEMENTS

New Announcements are Here.

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

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.

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 9:30 – 11 a.m. in FAC 332 Sign up for a workshop


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

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.
 * Join us at the CNS Summer Opportunities Workshop **

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

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

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.
 * 2015 Texas Student Research Showdown Final Round **

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). T he whole campus is invited to attend and watch the s ix 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.

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

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.
 * Is Grad School For Me?**

The Protein Society: Member Mini Grants <span style="color: #6700ce; font-family: Georgia,serif; font-size: 25px; line-height: 0px; overflow: hidden;"> 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.

<span style="color: #1155cc; font-family: arial,sans-serif;">@http://www.proteinsociety.org/join/benefits/minigrants/

<span style="color: #6700ce; font-family: Georgia,serif; font-size: 25px;">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 __

<span style="color: #6700ce; font-family: Georgia,serif; font-size: 25px;">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**

<span style="color: #6700ce; font-family: Georgia,serif; font-size: 25px;">Welcome back students! New Fall 2015 Research Conferences Update

__ **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

__**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

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

<span style="color: #6700ce; font-family: Georgia,serif; font-size: 25px;">The 29th Annual Symposium of The Protein Society

//<span style="color: #0f031b; font-family: Georgia,serif; font-size: 15px;">July 22-25, 2015 //
<span style="background-color: #ffffff; color: #333333; font-family: 'Benton Sans RE',Helvetica,sans-serif; font-size: 11.9999990463257px;">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!

<span style="background-color: #ffffff; color: #333333; font-family: 'Benton Sans RE',Helvetica,sans-serif; font-size: 11.9999990463257px;">For more information please visit the Protein Society Annual Meeting webpage here: http://www.barcelocongresos.com.es/protein2015/welcome.html



//<span style="color: #0f031b; font-family: Georgia,serif; font-size: 15px;">Tuesday, April 28, 2015 //
<span style="background-color: #ffffff; color: #333333; font-family: 'Benton Sans RE',Helvetica,sans-serif; font-size: 12px;">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.

<span style="color: #333333; font-family: Georgia,serif; font-size: 15px;">**Congratulations** to __Xenia Gonzalez__ for her nomination and to __Luis Valencia__ and __Oscar Villarreal__ for their awards!



<span style="color: #c96831; font-family: Arial,Helvetica,sans-serif; font-size: 1.3em; line-height: 1.5;">Success at the 2015 Undergraduate Research Forum
Visit this link for further info and full list of winners: <span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif; font-size: 12.8000001907349px;">@https://cns.utexas.edu/innovative-education/undergraduate-research/undergraduate-research-forum/awards-honors
 * A big congratulations to VDSers Serena Zadoo and Antonio Garcia on their awards! Serena was awarded the <span style="background-color: #ffffff; color: #333333; font-family: 'Benton Sans RE',Helvetica,sans-serif; font-size: 12px; line-height: 18px;">__CNS Award for Excellence in Biochemistry Research__ and Antonio the __SURGe Award for Most Interesting Research Poster__. **

** Intellectual Entrepreneurship (IE) Citizen Scholars Hosts 4th Annual Research Contest **
<span style="font-family: Arial,Helvetica,sans-serif;">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.


 * <span style="font-family: Arial,Helvetica,sans-serif;">Congratulations to VDSer //Xenia Gonzalez// ****<span style="font-family: Arial,Helvetica,sans-serif; line-height: 1.5;">for winning second place overall with her poster ****<span style="font-family: Arial,Helvetica,sans-serif; line-height: 1.5;">"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!
<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Class Location and Time: **BUR 216** on Tuesdays 3:30 - 4:30

Experiment Schedule and Due Dates for Assignments: Spring 2015
media type="custom" key="27118992"

=<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Buy a Lab Notebook: =
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Blueline notebooks (A9Q or A9, with or without grids, __192 pages__ costs $5.95) from the COOP
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">[[image:LabNotebookImage_outside.jpg width="480" height="270"]] [[image:LabNotebookImage_inside.jpg width="480" height="275"]][[image:vdsstream/LabNotebookImage_insidepages.jpg width="480" height="270"]]

<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">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 ICMB Core Facilities:
 * NHB glassware shop - next to BioSci storeroom
 * 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

<span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">40 points - prebuild <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">30 points - onsite build <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">30 points - exam

<span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">LINK TO THE BUILD ENVIRONMENT <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">Pre-Build FOK1 2fok.pdb. [|__http://cbm.msoe.edu/scienceOlympiad/designEnvironment/prebuild.html__]

<span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">OnSite Build Model [|__http://cbm.msoe.edu/scienceOlympiad/designEnvironment/regional.html__]

CHANGES! <span style="background-color: transparent; color: #000000; font-family: Arial; font-size: 15px; text-decoration: none; vertical-align: baseline;">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 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.
 * Undergraduate Research Forum VDS Poster**

2014 Fall Stuff below
@http://igem.org/Main_Page iGem info session Wednesday Dec. 10th, 5 pm in WEL 2.122
 * iGEM**
 * Interested in synthetic biology - cloning, etc.?**

ABRCMS! San Antonio
Oscar V. and Vicky G. presented their work Oscar brings home some hardware (or rather paperware and money)!

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 ICMB Core Facilities:
 * NHB glassware shop - next to BioSci storeroo
 * 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
- continue cloning target and move towards protein work and virtual work.
 * For Veterans**

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
 * For Returning Springers**

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'

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

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 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 = <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">Hey VDSers! <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">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 <span class="aQJ" style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">April 6th <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">would be a great social! The movie is free on campus and starts at 6. We'll probably head over at <span class="aQJ" style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">5:30 <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;"> 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! <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">-Priya <span style="background-color: #ffffff; color: #444444; font-family: 'Open Sans','Lucida Grande','Segoe UI',Arial,Verdana,'Lucida Sans Unicode',Tahoma,'Sans Serif'; font-size: 13.63636302947998px;">=)

WIRED SuperBug: =Serious Resistant Infections Increasingly Found in Children= @http://www.wired.com/wiredscience/2014/03/serious-resistant-infections-increasingly-found-children/

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
include component="page" wikiName="vdsstream" page="ExperimentScheduleVDSSp14"

LONGHORN RUN
<span style="font-family: comic sans ms,sans-serif;"> 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 <span class="aQJ" style="font-family: comic sans ms,sans-serif;">February 7th <span style="font-family: comic sans ms,sans-serif;"> and get 20% off registration fees when you use the "**EARLYBIRD**" (ALL CAPS) code. The race is on <span class="aQJ" style="font-family: comic sans ms,sans-serif;">**Saturday, April 12th** at **8:00 AM** <span style="font-family: comic sans ms,sans-serif;"> and it starts/finishes outside Gregory Gym.

<span style="font-family: comic sans ms,sans-serif;">To register with Team FRI: <span style="font-family: comic sans ms,sans-serif;">1) Go to this link: @https://www.edsregistration.com/events/64

<span style="font-family: comic sans ms,sans-serif;">2) Choose a distance; 2 mile or 10K <span style="font-family: comic sans ms,sans-serif;">3) Enter “FRI” in the line that says "List 1 student organization you are affiliated with" <span style="font-family: comic sans ms,sans-serif;">4) Use the code “EARLYBIRD” (case sensitive) for 20% off race fees <span style="font-family: comic sans ms,sans-serif;">Follow the event on FB for team updates and announcements.

<span style="font-family: comic sans ms,sans-serif;">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!
<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Class Location and Time: **BUR 216** on Tuesdays 3:30 - 4:30

__Things to start working on by the first week of class:__
<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">**Read the Syllabus**:
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">see link on left hand side menu '**Syllabus**'

<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Lab Safety Training:

 * Start completing your __online__ lab safety training: <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">see link on left hand side menu '**Required Lab Safety**'


 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Lab Safety Walk Throughs for this 1st Week (Meet in Lab PAI 2.14) . <span class="wiki_link_ext">**Sign Up Sheet**
 * <span style="font-family: Calibri,sans-serif; font-size: 12pt;">(NOTE: this also has sign up for the non-mandatory Help Sessions for Literature Search Assignment)

<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Lab Scheduling

 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Please fill out this: '**SchedulingVDSClassforGDocsSpring14forGDocs**' - see the Canvas page for this link
 * **<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">@Voluntary Buffers and Solution Sign-Up **
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">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)
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">you will need to have already done the Lab Safety Walk Throughs

=<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Buy a Lab Notebook: =
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">Blueline notebooks (A9Q or A9, with or without grids, __192 pages__ costs $5.95) from the COOP
 * <span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">[[image:LabNotebookImage_outside.jpg width="480" height="270"]] [[image:LabNotebookImage_inside.jpg width="480" height="275"]][[image:vdsstream/LabNotebookImage_insidepages.jpg width="480" height="270"]]

<span style="font-family: 'Times New Roman','serif'; font-size: 13.3333px;">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: []

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, <span style="font-family: arial,helvetica,sans-serif;">@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

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

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

Be cool and get the mobile App for ICM for your iPhone (iTrash) or Android.
@http://www.molsoft.com/iMolview.html

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">The Rise of Neglected Tropical Diseases and Poverty in Developing <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">Countries and the Southern United States with Dr. Peter Hotez Tuesday, October 1, 2013 5:45 PM **- networking time**
 * <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">COOL TALK: **
 * Actual talk starts at 6:30 pm**
 * Location:** AT&T Executive Education and Conference Center Amphitheater (Room 204)

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">REGISTER: <span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif;">@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/

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

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

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

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

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



7/1/13 - Pics of VDSers are in the Google Docs/Pics folder
@http://f1000.com/resources/Negative_Results_PR_WEB.pdf
 * What is 'publication bias'?**

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!
<span style="background-color: #ffffff; color: #333333; font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 12px;">Life Technologies Award for Excellence in Biochemistry Research ($500)

<span style="background-color: #ffffff; color: #333333; font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 12px;">Kaarthik Rajendran

<span style="background-color: #ffffff; color: #333333; font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 12px;">SURGe Students’ Choice Award Honorable Mention ($50) <span style="background-color: #ffffff; color: #333333; font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 12px;">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:
<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">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. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">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. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">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). 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.
 * <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">Chemistry and Biochemistry Majors **
 * Biology Majors**
 * Public Health Majors**

ASSIGNMENT DUE DATES: (updated 4/22/13)
changed to Sunday Mar 31st @ midnight || Lab Report: Virtual Screening 1 || Changed to Wed (April 17th) @ mn || Lab Report (Online): Protein Labs Combined ||
 * **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
 * Mon (3/25 ) changed to Thursday Mar 28th @ midnight
 * Mon (3/25 ) changed to Thursday Mar 28th @ midnight
 * Sat (April 13th) @ 5pm || Lab Notebook due (VS2 & Protein Characterization) ||
 * Mon (April 15th) @ mn
 * 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 ||
 * T.B.D. || Lab Safety Quiz on BB ||

**Journal Club Article for 14th Class**
(print out and bring to class)

Pre-class Questions (answer and bring to class)

Longhorn Run Results:
[]





<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">**Monday, April 15th** <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">**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. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">The scheduled panelists are: <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">Dr. Gregory Daniel Frank, Ph.D., Director of Business Development, XBiotech <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">Dr. Jeanette Hill, Ph.D., Founder and CEO, Spot on Sciences <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">Nichole Wiedemann, Associate Dean for Undergraduate Programs (UT School of Architecture), Associate Professor <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.3333px;">Dr. Barbara Brown Wilson, Director, Center for Sustainable Development (UT School of Architecture), Associate Professor



Longhorn Run
Packet Pickup in Gregory Gym Thursday, Friday If you have any questions, please email eghanem3@gmail.com. See you all on Sat! Go Team FRI!
 * 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!

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 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.

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

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

Longhorn Run:
<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.333333969116211px;">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 <span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif; font-size: 13.333333969116211px;"> FB event page <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.333333969116211px;">. Please share with your students. Let me know if you have any questions.

[]NOTE: 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)
 * <span style="color: #333333; font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 12px;">College of Natural Sciences Summer Research Fellowships (FRI summer research) **

LabNotebookD Grade statistics:

 * AVG || 9.30 ||
 * MAX || 10.00 ||
 * MIN || 7.10 ||
 * STDEV || 1.29 ||
 * MEDIAN || 9.7 ||



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



@Mid Semester Meetings with Dr B

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)

<span style="background-color: #ffffff; font-family: arial,sans-serif; font-size: 13.513513565063477px;">Monday (3/4) from 6-8 in Welch Computer Lab --- Daniel is the mentor

<span style="background-color: #ffffff; font-family: arial,sans-serif; font-size: 13.513513565063477px;">Tuesday (3/5) from 6-8 <span style="background-color: #ffffff; font-family: arial,sans-serif; font-size: 14px;"> 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

<span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif;">Class Average: **9.13** STDEV: **+/- 1.68** Max grade: **10** Lowest Non-zero: **7.60** Median grade: **9.4**
 * Lab Notebooks (022812):**

**GOLD STAR AWARDS**: <span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif;">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.



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 ||
 * S L Wolf ||
 * Mr. Kaarthik Rajendran ||
 * Jiaqi Zhang ||
 * Ariel Chen ||
 * Ariel Chen ||
 * Ariel Chen ||
 * Ariel Chen ||

==

Longhorn Run
FRI Runners!

Team members are invited to **Victory @ Gregory Gym** on 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 <span style="background-color: #ffffff; color: #1155cc; font-family: arial,sans-serif; font-size: 13.333333969116211px;">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!
 * Thursday 2/14 at 5:30 PM** for the official announcement of the winner of the

Join Team FRI:
<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">The team that registers most runners by ** Feb 13th **<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;"> wins customized race day t-shirts. 1) Go to this link: http://www.edsregistration.com/races/256/registrations/new?team_id=1023

<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;"> The race is on Saturday, April 13th at 8:00 AM. To register with Team FRI: <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">2) Choose a distance; 2 mile or 10K <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">3) Enter “**FRI**” in the line that says “Please List 1 student organization you are affiliated with”. <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif;">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.

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__

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Lab Notebooks: <span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif;">Class Average: **8.49**STDEV: +/- 0.71Max grade: 9.70Lowest Non-zero: 6.2Median grade: 8.6

<span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif;"> GOLD STAR awards:We also had 4 gold star awards for exemplary notebooks! Congratulations to:**Serena Z****Kavya K****Young L.****Ashlee W**

Schedule (PyMol1) - in Computer Lab
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Help Sessions: Excel Setup & Analysis
<span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif; font-size: 13.2px;">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 pm****FRIDAY: 3:30 - 5 pm**

<span style="background-color: #ffffff; color: #222222; display: block; font-family: arial,sans-serif; font-size: 13.2px;">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!
<span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.200000762939453px;">DATE: Wednesday, January 23, 2013 <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.200000762939453px;">TIME: 9am – 2pm (or while supplies last) <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.200000762939453px;">LOCATION: Student Services Building Glenn Maloney Room (SSB G1.310) <span style="background-color: #ffffff; color: #222222; font-family: arial,sans-serif; font-size: 13.200000762939453px;">(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!

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FALL 2012 Stuff Below:
Link to form [] Results to form media type="custom" key="21692140"

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

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

Final Report Guidelines (due Sat Dec 8th)

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. 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: [] Upload Passwerd: same as our GDocs
 * UTEID_Name_Date_AssignmentName.doc **

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: []

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



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/)

110512 - <span style="font-family: arial,helvetica,sans-serif;">**Undergraduate Research Journal (URJ) at UT-Austin**. <span style="display: block; font-family: arial,helvetica,sans-serif; font-size: 13px;">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).**
 * P**anelists with PhDs in the Chemical and Biological sciences.

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.

@http://www.austinforum.org/ 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..)
 * 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:
 * Thursday, November 8th at 6:30 pm** in the AT&T Conference center

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





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



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 - 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



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



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**



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

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.

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.
 * 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)

END SPRING - SUMMER 2012 ANNOUNCEMENTS

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

Register: [| https://ricemba.wufoo.com/forms/ra-austin-chapter-distinguished-professor-event/]
Wear Business Casual Attire



072612 - Thursday 3:00 - GASF (Genome Sequencing and Analysis Facility) Tour in MBB 4.102
Paper to read before the tour:

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

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 viewing**


 * 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 ......

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.

[]

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.



<span style="color: #67a7e3; display: block; font-family: arial,sans-serif; font-size: 12px; text-align: left;">[]

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 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)

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

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

include component="page" wikiName="vdsstream" page="Forum Presentation Times"

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





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

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

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.

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 ||
 * || 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 ||
 * || 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 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



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!**



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
 * [[file:vdsstream/LiteratureAssignment_VDSSpring2012.docx|LiteratureAssignment_VDSSpring2012.docx]] -DUE: Mon Jan 23rd
 * [[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]**File Not Found**

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

 * worth 1 quiz for points
 * @https://survey.grinnell.edu/se.ashx?s=251137450D92E7A6
 * enter "Beckham" as Instructor and "CH204" for the Course (since this is the main course that they are linked under)

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

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.

__HOURS__
Fig. 1. VDS class Lab Hours. Average is for semester-to-date. Week 11 **<span style="font-family: 'Times New Roman','serif';">(11/7 – 11/11) **

__**Research Presentation Schedule:**__ RE digest and Nanodrop: **Marshall** || - include Codon Optimization Gel electrophoresis (mainly for DNA but also protein): **J.C.** || **Larry** ||= pNIC-Bsa4 LIC cloning: **Joshua** || Characterization: **Indra** || Johnny ||=  ||
 * ~  ||~ **Research** ||~ **Technique** ||
 * = Aug 30th ||= none ||= none ||
 * = Sept 6th: ||= **Krishna, Sadhana** ||= DNA sequencing/Analyze DNA sequence: **Joey**
 * = Sept 13th ||=  ||= PCR and Overlap PCR: **Justin**
 * = Sept 20th ||= **Indra,**
 * = Sept 27th ||= Journal Club ||= Midiprep/Miniprep: **Sadhana** ||
 * = Oct. 4th ||= **Marshall, Justin** ||= Transformation, Expression - bacterial growth: **Larry** ||
 * = Oct. 11th ||= Journal Club ||= **P**urification: **Krishna**
 * = Oct. 18th ||= **J.C., Joshua** ||= Enzyme Assay: **Hong** ||
 * = Oct. 25th ||= <span style="color: #000000; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Journal Club, <span style="color: #0070c0; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Chijiioke, Jericho ||=  ||
 * = Nov. 1st ||= Joey, Michael,, Hong ||=  ||
 * = Nov. 8th ||= Journal Club, Ronnie, <span style="color: #0070c0; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Mohammed,
 * = Nov. 15th ||= Shreya, T.J., <span style="color: #0070c0; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Giancarlo, ||=  ||
 * = Nov. 22nd ||= <span style="color: #000000; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Shutian

<span style="color: #000000; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Journal Club 6 ||  || 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**
 * = Nov. 29th ||=  ||= Presentations of Final Results (Inhibition <span style="color: #000000; display: block; font-family: Arial; font-size: 16px; text-align: center; vertical-align: baseline;">Assay Graphs) ||
 * Instructions**: prepare 5-10 Powerpoint slides to present your work to date
 * **Intro (talk about your disease and what your protein does)**, **Objectives**, **Methods& Results**, **Future Directions**
 * Guidelines:**
 * <span style="font-family: Arial,Helvetica,sans-serif;">prepare a 10 minute powerpoint slide show
 * <span style="font-family: Arial,Helvetica,sans-serif;">Start out with a title slide that has the Title and Your Name on it
 * <span style="font-family: Arial,Helvetica,sans-serif;">Create an introduction that provides a broad perspective for the disease being presented. Then provide some background on the protein and what it does.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Talk about the methods you used - why did you do certain steps?
 * <span style="font-family: Arial,Helvetica,sans-serif;">Talk about any mistakes or failures that would help other in the class.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Make an effort to explain what is going on in the figures
 * <span style="font-family: Arial,Helvetica,sans-serif;">Include a caption
 * You can also make your own cartoons and schematic diagrams or show relevant pictures
 * <span style="font-family: Arial,Helvetica,sans-serif;">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.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Talk about your immediate next steps
 * <span style="font-family: Arial,Helvetica,sans-serif;">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.
 * <span style="font-family: Arial,Helvetica,sans-serif;">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. 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: =Undergraduate Research Grant= = = =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.
 * =  ||= Thursday Oct 25th ||= Friday Oct 26th ||= Saturday Oct 27th ||
 * = 1 ||= Michael E. ||=  ||=   ||
 * = 2 ||=  ||=   ||=   ||
 * = 3 ||= T.J. ||=  ||=   ||
 * = 4 ||=  ||=   ||=   ||

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

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

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: 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.
 * Monday 4 - 5:30 in WEL 2.306 Computer Lab.

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

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 Science Works Assignment: create a profile. Here is a
 * Thursday Sept 15th: 4 -6 pm
 * **Monday Sept 19th: 5-7 pm**

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

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

<span style="background-color: transparent; color: #000000; font-family: serif; font-size: 16px; text-align: start; text-decoration: none; vertical-align: baseline;">Interesting __<span style="background-color: transparent; color: #0000ee; font-family: serif; font-size: 16px; text-align: start; vertical-align: baseline;">article __ on antibiotic resistance. <span style="background-color: transparent; color: #000000; font-family: serif; font-size: 16px; text-align: start; text-decoration: none; vertical-align: baseline;">1st Part of the Last 2 Labs: Virtual Screening 3 protocol: <span style="background-color: transparent; color: #000000; font-family: serif; font-size: 16px; text-align: start; text-decoration: none; vertical-align: baseline;">2nd Part of the Last 2 Labs: Enzyme Inhibition Assay handout: and protocol: <span style="background-color: transparent; color: #000000; font-family: serif; font-size: 16px; text-align: start; text-decoration: none; vertical-align: baseline;">The Pre-class Questions for the Journal Paper discussion on Tuesday can be found here. <span style="background-color: transparent; color: #000000; font-family: serif; font-size: 16px; text-align: start; text-decoration: none; vertical-align: baseline;">PTP1b virtual screening paper: Read before the last 2 labs. media type="custom" key="9115208"

> __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: > > > See the Forum Presentation Times for your assigned time > > Sign up sheet for Poster Session at the Undergraduate Research Forum Friday April 8th > > Handout: LabProteinPurificationVDS_Spring11.docx > PTP1b virtual screening paper: Read before the last 2 labs. ParkStructureBasedVirtualScreen_PTP1B_EuJMedChem2009.pdf > > ****Next Step Central**** ( Assignment due Tues March 22nd) > Summer FRI Fellowships Application (Application date: Tues March 22nd >
 * We will be doing the **Protein Characterization Lab** for next week. We will work in **pairs** as much as possible.
 * Handout: [[file:LabVirtualScreen2VDS_Spring11.doc]] NOTE: the first version of this had the WRONG due date. This is now changed - it is April 11th Monday.
 * Handout: [[file:LabVirtualScreen2VDS_Spring11.doc]] NOTE: the first version of this had the WRONG due date. This is now changed - it is April 11th Monday.
 * Handout: [[file:LabVirtualScreen2VDS_Spring11.doc]] NOTE: the first version of this had the WRONG due date. This is now changed - it is April 11th Monday.
 * Handout: [[file:LabVirtualScreen2VDS_Spring11.doc]] NOTE: the first version of this had the WRONG due date. This is now changed - it is April 11th Monday.
 * 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)
 * 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)**

 * || **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 ||   ||   ||   ||   ||