Timeline+F14

=TIMELINE FOR RESEARCH= NOTE - see bottom of page for previous weeks' schedules and things to catch up on. Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window. @Daily Schedule Summ14 @Timeline F13

Looking for the **Presentation Schedule**? - see the Schedule Fall14 ( Semester) Link to Research Progress Table Wikispaces check on every other Sunday (Bi-weekly) Class slides are uploaded to CANVAS after each class.
 * This also has the Presentation Guidelines for all 3 types of presentations: Research Presentations, Technical Presentations, Journal Club Presentations


 * ===** This Week **=== || ===** This Week **=== ||
 * **WEEK15 - final week**

Peer Reviews - should already have these done
 * Peer Review of Research Report on Target (Mid semester) - 1 per person
 * Peer Review of M&M Cloning - 2 per person
 * Peer Review of M&M Virtual- 2 per person
 * SKIP: peer review of M&M Expr, Pur, Char

finish cloning
 * Wet Lab work**

express a FtHap protein if finished with at least 3 cloning attempts


 * Virtual Work**
 * - analyze scores
 * ---InHouseCompounds (~40 ligs) -use 1 processor
 * ---CB306 (306 ligs) - use 1 processor
 * ---NIHClinicalCollection (446 ligs), use 1 processor
 * ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor

class FRI Survey (10-20 min) @https://utexas.qualtrics.com/SE/?SID=SV_6G8NU0TAFlSWawJ
 * 1-Dec Monday**
 * 2-Dec Tuesday**
 * 3-Dec Wednesday**

Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard Final Lab Report Due @ 9pm
 * 4-Dec Thursday**
 * 5-Dec Friday**
 * 6-Dec Saturday**


 * 7-Dec Sunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 14, 15)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y'**

Final Lab Notebook Due at 9pm || **WEEK15 - final week**
 * Monday Dec 8th -**

Peer Reviews - should already have these done
 * Peer Review of Research Report on Target (Mid semester) - 1 per person
 * Peer Review of M&M Cloning - 2 per person
 * Peer Review of M&M Virtual- 2 per person
 * SKIP: peer review of M&M Expr, Pur, Char


 * Enzyme Assays & Inhibition Assays**
 * determine if your enzyme is active
 * determine how much enzyme to use to get 'good' absorbance signal
 * vary amount of substrates(s) to optimize assay
 * Dilute inhibitors in DMSO
 * test out inhibitors (vary concentration)


 * Virtual Work**
 * - analyze scores

class FRI Survey (10-20 min) @https://utexas.qualtrics.com/SE/?SID=SV_6G8NU0TAFlSWawJ
 * 1-Dec Monday**
 * 2-Dec Tuesday**
 * 3-Dec Wednesday**

Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard Complete your 30 min of lab cleanup either today or tomorrow - see sheet on whiteboard Final Lab Report Due @ 9pm
 * 4-Dec Thursday**
 * 5-Dec Friday**
 * 6-Dec Saturday**


 * 7-Dec Sunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 14, 15)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y'**

Final Lab Notebook Due at 9pm || Wikispaces posting due - Sundays at 9 pm Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y'** This page will run in reverse chronological order - i.e. Newest stuff on top Wiki postings should be a sort of highlights of results page. You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc. You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.). You should have enough information in the captiont to let the reader (Dr. B) understand what it is.
 * Monday Dec 8th -**
 * SPRINGERS || VETERANS ||
 * ===** Next Week **=== || ===** Next Week **=== ||
 * **RECURRING ITEMS:**
 * ===** Next Week **=== || ===** Next Week **=== ||
 * **RECURRING ITEMS:**
 * **RECURRING ITEMS:**
 * **RECURRING ITEMS:**
 * Below that** add your 'result' image for the week with brief commentary


 * Lab Notebook check** - Saturdays at 5pm

REQUIRED ITEMS FOR NOTEBOOKS: All practice cloning work (including well labelled gels) Protein work (esp protein gel and FPLC output and nanodrop) We definitely need all of your Target work to be present in the notebook.
 * DNA Works Output file - print the text file and past in notebook
 * Tail Primer Design (protocol and what you designed)
 * Info from your Target Page (which means you need a Target page first!)

Update **Target** page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target.

Cut pNIC-Bsa4 that you grew up with BsaI (part of pNIC-Bsa4 Cloning protocol), gel check
 * ITEMS FOR LATER:**

Tail Primer Design and Ordering

ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones)
 * Make LB+Kan plates (4) -**

ProtocolLBAgarPlatesVDS.doc (not the Kan/Suc ones) ||  ||
 * Make LB + Kan/Suc plates (6)**

After Fire Safety Training is uploaded: PAPER COPY – Print out of **TxClass Safety Training -**  - (can put in Safety section of VDS sign-in binder in lab)

Nanodrop & Submit to DNA Sequencing (1.5 hrs) Target Selection Form
 * Project Tasks (in rough order)**:

Dilute some primers from lyophilized powder: random ones (pLIC-for & pLIC-rev)? -- make working dilution in water from 100uM stock. -- Store working dilution in YOUR own box.

Make 500ml of LB and autoclave (with mentor) Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5

Midi-prep (in pairs) - use Tony's new protocol Input information about which culture of plasmid you have (or will) grow up. @https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing Submit to DNA Sequencing for YOUR pNIC-Bsa4 that you grew up
 * GoogleDocs/Misc/Plasmid Concentrations**

Analyze DNA Sequence Exercise (as a group)

Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
 * upload final primers to Google Docs/VDS/Misc/Primers/**PrimerPlateOrderFall2014**
 * post final primers to Wikispaces Target page

'My Second PCR' - PCR pLIC using pNIC-Bsa4 Set up target protein for Virtual Screening

Design Tail Primers for targets, order tail primers Primer Dilution or your own primers

Create or Revise your Target page (not same as you Research Page) LICpNIC-Bsa4cloningExerciseVDS_Fall14

Make Oligo mix for Targets

Expression Purification Characterization Enter your **protein yields** into: Protein Spectrophotometer Calc @https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodC1mRVpNLVlDOUE4NlNxdldqNEZwRmc&usp=sharing
 * PROTEIN INFO**

CB Diversity (50K ligs) screening Due Cloning Materials & Methods due @ ??? -- see guidelines on GDocs
 * Virtual Work**
 * M&M's**

Peer Review of M&M Cloning is due @ ??? - you will have 2 to review - make 5 constructive criticisms - make 2 compliments

Virtual M&M due @ ??? Expression, Purification, Characterization M&M due @ ??? -- see guidelines on GDocs

M&M Virtual
 * Peer Review due ??:**

M&M Expression, Pur, Char
 * Peer Review due ??:**

Finish virtual screening Enzyme Assay protocol Inhibition Assay protocol

Week1&2 Hrs Week 3&4 Hrs ...... LabNotebook A, B, C, D
 * Graded Assignments:**
 * HOURS:**

Wikispaces (Bi-Weekly) WikiWeek1&2

Safety Target Page LICpNIC-Bsa4cloningExercise Journal Club presentation and Question sheets Technical Presentation (if applicable) Research Presentation PyMol Refresher Virtual Screening Refresher Mid-Semester Research Report on Target Draft of M&M Cloning Draft of M&M Virtual Draft of M&M Express,Pur,Char Final Report

**2 Weeks Blocks layout**

 * Week1 || 25-Aug || Monday || 29-Aug || Friday ||
 * Week2 || 1-Sep || Monday || 5-Sep || Friday ||
 * Week3 || 8-Sep || Monday || 12-Sep || Friday ||
 * Week4 || 15-Sep || Monday || 19-Sep || Friday ||
 * Week5 || 22-Sep || Monday || 26-Sep || Friday ||
 * Week6 || 29-Sep || Monday || 3-Oct || Friday ||
 * Week7 || 6-Oct || Monday || 10-Oct || Friday ||
 * Week8 || 13-Oct || Monday || 17-Oct || Friday ||
 * Week9 || 20-Oct || Monday || 24-Oct || Friday ||
 * Week10 || 27-Oct || Monday || 31-Oct || Friday ||
 * Week11 || 3-Nov || Monday || 7-Nov || Friday ||
 * Week12 || 10-Nov || Monday || 14-Nov || Friday ||
 * Week13 || 17-Nov || Monday || 21-Nov || Friday ||
 * Week14 || 24-Nov || Tuesday || 28-Nov || Friday ||
 * Week15 || 1-Dec || Monday || 5-Dec || Friday ||




 * || **WEEK1**
 * WEEK2**
 * WEEK3**
 * WEEK4**
 * WEEK5**
 * WEEK6**
 * WEEK7**
 * WEEK8**
 * WEEK9**
 * WEEK10**
 * WEEK11**
 * WEEK12**
 * WEEK13**
 * WEEK14**
 * WEEK15** ||
 * **8-Dec Monday**
 * 9-Dec Tuesday**
 * 10-DecWednesday**
 * 11-DecThursday**
 * 12-DecFriday**
 * 13-DecSaturday**
 * 14-DecSunday**
 * 15-DecMonday**
 * 16-DecTuesday** || **8-Sep Monday**
 * 9-Sep Tuesday**
 * 10-SepWednesday**
 * 11-SepThursday**
 * 12-SepFriday**
 * 13-SepSaturday**
 * 14-SepSunday**
 * 15-SepMonday**
 * 16-SepTuesday**
 * 17-SepWednesday**
 * 18-SepThursday**
 * 19-SepFriday**
 * 20-SepSaturday**
 * 21-SepSunday**
 * 22-SepMonday**
 * 23-SepTuesday**
 * 24-SepWednesday**
 * 25-SepThursday**
 * 26-SepFriday**
 * 27-SepSaturday**
 * 28-SepSunday**
 * 29-SepMonday**
 * 30-SepTuesday**
 * 1-Oct Wednesday**
 * 2-Oct Thursday**
 * 3-Oct Friday**
 * 4-Oct Saturday**
 * 5-Oct Sunday**
 * 6-Oct Monday**
 * 7-Oct Tuesday**
 * 8-Oct Wednesday**
 * 9-Oct Thursday**
 * 10-OctFriday**
 * 11-OctSaturday**
 * 12-OctSunday**
 * 13-OctMonday**
 * 14-OctTuesday**
 * 15-OctWednesday**
 * 16-OctThursday**
 * 17-OctFriday**
 * 18-OctSaturday**
 * 19-OctSunday**
 * 20-OctMonday**
 * 21-OctTuesday**
 * 22-OctWednesday**
 * 23-OctThursday**
 * 24-OctFriday**
 * 25-OctSaturday**
 * 26-OctSunday**
 * 27-OctMonday**
 * 28-OctTuesday**
 * 29-OctWednesday**
 * 30-OctThursday**
 * 31-OctFriday**
 * 1-Nov Saturday**
 * 2-Nov Sunday**
 * 3-Nov Monday**
 * 4-Nov Tuesday**
 * 5-Nov Wednesday**
 * 6-Nov Thursday**
 * 7-Nov Friday**
 * 8-Nov Saturday**
 * 9-Nov Sunday**
 * 10-Nov Monday**
 * 11-Nov Tuesday**
 * 12-Nov Wednesday**
 * 13-Nov Thursday**
 * 14-Nov Friday**
 * 15-Nov Saturday**
 * 16-Nov Sunday**
 * 17-Nov Monday**
 * 18-Nov Tuesday**
 * 19-Nov Wednesday**
 * 20-Nov Thursday**
 * 21-Nov Friday**
 * 22-Nov Saturday**
 * 23-Nov Sunday**
 * 24-Nov Monday**
 * 25-Nov Tuesday**
 * 26-Nov Wednesday**
 * 27-Nov Thursday**
 * 28-Nov Friday**
 * 29-Nov Saturday**
 * 30-Nov Sunday**
 * 1-Dec Monday**
 * 2-Dec Tuesday**
 * 3-Dec Wednesday**
 * 4-Dec Thursday**
 * 5-Dec Friday**
 * 6-Dec Saturday**
 * 7-Dec Sunday**
 * 8-Dec Monday**
 * 9-Dec Tuesday**
 * 10-DecWednesday**
 * 11-DecThursday**
 * 12-DecFriday**
 * 13-DecSaturday**
 * 14-DecSunday**
 * 15-DecMonday**
 * 16-DecTuesday** ||


 * Target meetings:**


 * 1st one completed:**


 * Primer Ordering Instructions (date?)**

Everyone designs their primer - but we will only order one person's set. Be sure you use the correct DNA Works output file to get your codon optimized DNA sequence (not just the CDS). -- If you are use a Summer plate - you need to get your DNA Works Output file from **Misc/Primers/DNAWorks_OutputSummer14** -- If you are use a Fall plate - you need to get your DNA Works Output file from **Misc/Primers/DNAWorks_OutputFall14**

Save the Word doc of your primer design into your GDocs Print Word doc and paste into your Lab Notebook Crosscheck your sequence with your Teammates Put the sequences of the Tail Primers on your team's target page. -- Enter your name for the person whose primers we will order - once you have designed the primers Put the info and sequence on the Target Spreadsheet

https://docs.google.com/spreadsheet/ccc?key=0AvGl3lMyhDsodDJlZDlneXMtb1JuREV0MUZQYXU4YkE#gid=0

Order your primers -- go to the ICMB core site (see our Targets Spreadsheet for the link) -- find the IDT link -- enter our username: VDS (all caps) and password: same as the password to get on to the laptops buildingname+labroomnumber --Products/DNA/RNASynthesis/CustomDNAOligos --select 2 for the Multiple Entry -- leave defaults for Scale and Purification -- enter your 2 primers and the Prefixes. -- save to Wishlist, Dr. B will order when we have several of them. class sign up for Fire Safety training (see link to left 'Required Lab Safety') Lab times open for Nanodrop and Submit to DNA sequencing
 * **WEEK1**
 * 25-Aug Monday**
 * 26-Aug Tuesday**
 * 27-Aug Wednesday**
 * 28-Aug Thursday**

Link to create dnaLIMS Account: (***must make an account before submitting DNA to sequencing)**
 * @http://146.6.133.14/cgi-bin/dna/loginNn.cgi **


 * --- sign up on sheet above**

Nanodrop protocol Submit to DNA Sequencing

29-Aug Friday 30-Aug Saturday 31-Aug Sunday || WEEK1 25-Aug Monday 26-Aug Tuesday 27-Aug Wednesday 28-Aug Thursday 29-Aug Friday 30-Aug Saturday 31-Aug Sunday || Be sure you have 8-10hrs/week
 * class**
 * sign up for Fire Safety training (see link to left 'Required Lab Safety')**
 * startup your cloning work again**
 * SPRINGERS WEEK2
 * - for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days**
 * For this week, you need about 6.5-8 hrs.**

ITEMS TO DO THIS WEEK**
 * sign up for Fire Safety training (see link to left 'Required Lab Safety')
 * Create your own folder in Google Docs under the folder: ** /StudentFolders **
 * Make 500ml of LB and autoclave (with mentor) - anytime mentor available
 * Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) - at specific times
 * -- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5.doc
 * Dilute some primers (if they come in) - anytime mentor available
 * Target Selection Form - once Dr. B sends the link
 * Analyze DNA Sequence Exercise (as a group) - at specific times (this week or next depending on Target Selections and Primer Design)
 * (maybe) RE Digest - at specific times


 * 1-Sep Monday - LABOR DAY - no lab**
 * 2-Sep Tuesday**

Transformation times at 3:30 PM (must start on time) Make 500ml of LB and autoclave (with mentor)

class
 * 3-Sep Wednesday**

Transformation times at 3:30 PM (must start on time) Make 500ml of LB and autoclave (with mentor)


 * 4-Sep Thursday**

Make 500ml of LB and autoclave (with mentor) Dilute some primers (if they come in) Transformation times at 5:30 PM (must start on time)


 * 5-Sep Friday**

1:30-4:30 pm Analyze DNA Sequence Exercise (as a group) OR Primer Design if Targets figured out Make 500ml of LB and autoclave (with mentor) Dilute some primers (if they come in)


 * 6-Sep Saturday**
 * Lab Notebook check** - Saturday at 5pm

Nanorop - 2 images for Wiki & protocol/images in Notebook Submit to DNA - protocol in Notebook, if have result - put in Notebook too Wet lab and virtual work should go into notebook Oligo Design - upload output file to GDocs, paste Oligo sequence into your Target page, in Notebook too Analyze DNA Sequence - upload results to GDocs (put the protocol in your Notebook - results can stay in GDocs) RE Digest - if done PCR & run on an agarose gel - images to Wiki & protocol/images in Notebook
 * What Goes Where for notebook?:**

Target page updates due - 9 pm - SKIP FOR THIS WEEK
 * 7-Sep Sunday**

Wikispaces posting due - 9 pm Add content to YOUR __research__ page on Wikispaces Put a line and **'Week 1&2'** This page will run in reverse chronological order - i.e. Newest stuff on top Wiki postings should be a sort of highlights of results page. You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc. You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.). You should have enough information in the captiont to let the reader (Dr. B) understand what it is. || **WEEK2** - for the 1st week of class that should be about 3-4hrs since the lab was only open for 2 days For this week, you need about 6.5-8 hrs.
 * Below that** add your 'result' image for the week with brief commentary
 * Be sure you have 8-10hrs/week**

class
 * 1-Sep Monday**
 * 2-Sep Tuesday**
 * 3-Sep Wednesday**

3-4 Zain & Hailey site specific training with Priya


 * 4-Sep Thursday**
 * 5-Sep Friday**


 * 6-Sep Saturday**
 * 7-Sep Sunday** ||
 * **WEEK3**


 * ITEMS TO DO THIS WEEK**
 * RE Digest of pGBR22
 * ProtocolRestrictionEnzymeDigestVDS.doc
 * Dilute some primers (if they come in) - anytime mentor available
 * Grow up your pNIC-Bsa4 colonies (DH5alpha) overnight
 * If failed last week, Re-transform pNIC-Bsa4 into DH5alpha (with a partner)
 * - use 'homemade' competent cells (NOT THE NEB ones) - at specific times
 * Target Selection Form - once Dr. B sends the link - SENT
 * Primer Design and Ordering
 * Create/Update Target pages
 * MAYBE: 'My First PCR' - using pGBR22
 * - ProtocolPCRVDS.xls

Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later. -Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan --pNIC-Bsa4 is a 'low copy' plasmid --spin down next morning (save in -20degC or proceed to Midi-Prep - 2-3hrs)

-- if you don't' have time to spin down in morning (~30-45 min), you can temporarily store your growth flask in 4degC for __a few hours__ til you can spin it in the afternoon. Pellets can be frozen and stored til next day or so.

In order to make lots of plasmid that we will need for cloning: -- Plasmid Midi-prep (in pairs) - use Tony's new protocol


 * 8-Sep Monday**
 * 9-Sep Tuesday**
 * FIRE SAFETY TRAINING for FRI Students only**
 * --** Speed Way in front of SAC (just show up and sign in)

Fill Out: __Target Selection Form__ @https://docs.google.com/spreadsheet/viewform?formkey=dHJITzhKOHVvMUhNU05TRE81NktjV0E6MA


 * 10-SepWednesday**

class

Target Selection Form


 * 11-SepThursday**

Create/Update Target page on Wikispaces for your Team's target Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
 * upload final primers to Google Docs/VDS/Misc/Primers/**PrimerPlateOrderFall2014**
 * post final primers to Wikispaces Target page


 * 12-SepFriday**

Create/Update Target page on Wikispaces for your Team's target Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall14.doc - 2 hrs
 * upload final primers to Google Docs/VDS/Misc/Primers/**PrimerPlateOrderFall2014**
 * post final primers to Wikispaces Target page


 * 13-SepSaturday**
 * 14-SepSunday** || **WEEK3**
 * 8-Sep Monday**
 * 9-Sep Tuesday**
 * FIRE SAFETY TRAINING for FRI Students only**
 * --** Speed Way in front of SAC (just show up and sign in)


 * 10-SepWednesday**

class


 * 11-SepThursday**

4- 8 pm PyMol Refresher Help Session in Computer Lab

PyMol Refresher due for Vets (less Zain, Hailey) can count as 2 hours of lab time
 * 12-SepFriday**


 * 13-SepSaturday**
 * 14-SepSunday** ||
 * **WEEK4**


 * ITEMS TO DO THIS WEEK**
 * Run gel of RE Digest of pGBR22
 * Agarose Gel protocol
 * Grow up your pNIC-Bsa4 colonies (DH5alpha) overnight (see below for steps)
 * Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)
 * 'My First PCR' - using pGBR22
 * - ProtocolPCRVDS.xls
 * PyMol Refresher

Grow up pNIC-Bsa4 in DH5alpha cells for Plasmid Preps
4:00 - 5 PM - start overnight cultures of plasmids in DH5alpha for midi prepping later. -Grow up pNIC-Bsa4 overnight in 160ml of LB + Kan --pNIC-Bsa4 is a 'low copy' plasmid --spin down **next morning (10-11 am) - make sure a mentor can be there!** (save in -20degC or proceed to Midi-Prep - 2-3hrs)

-- if you don't' have time to spin down in morning (~30-45 min), you can temporarily store your growth flask in 4degC for __a few hours__ til you can spin it in the afternoon. Pellets can be frozen and stored til next day or so.

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall14.doc


 * 15-SepMonday**
 * 16-SepTuesday**
 * 17-SepWednesday**
 * 18-SepThursday**
 * 19-SepFriday**
 * 20-SepSaturday**


 * Lab Notebook check** - Saturday at 5pm

Oligo Design - protocol and DNA Works output file Analyze DNA Sequence RE Digest PCR & run on an agarose gel (if done)
 * What Goes Where for notebook?:**

Wikispaces posting due - 9 pm Add content to YOUR __research__ page on Wikispaces Put a line and **'Week 3&4'** This page will run in reverse chronological order - i.e. Newest stuff on top Wiki postings should be a sort of highlights of results page. You should have nanodrop images, gel images, yields from protein purification, brief virtual results, etc. You don't need alot of lengthy description of the procedures - only figure captions and a brief analysis of the result (e.g. 1-2 sentences of why it did or didn't work, next steps, etc.). You should have enough information in the caption to let the reader (Dr. B) understand what it is. || **WEEK4**
 * 21-SepSunday**
 * Below that** add your 'result' image for the week with brief commentary


 * Wet Lab**
 * continue cloning, expression, purification, storage
 * look up your substrates and how to order them
 * look up enzyme assay in other research papers


 * Virtual Work**

start Virtual Screening Refresher - see GDocs/Protocols/VirtualProtocols

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall14.doc


 * 15-SepMonday**
 * 16-SepTuesday**
 * 17-SepWednesday**
 * 18-SepThursday**

Virtual Refresher Help Session

Virtual Refresher Help Session
 * 19-SepFriday**


 * 20-SepSaturday**


 * Lab Notebook check** - Saturday at 5pm


 * 21-SepSunday**

Wikispaces posting due - 9 pm ||
 * **WEEK5**


 * Repeat - 'My First PCR' - if failed
 * PyMol Refresher
 * Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)
 * Make Oligo Mix for your targets (each person makes own)
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx

This week or next (depends on your lab hours)
 * Primary PCR
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx
 * Midi-Prep your spun down pNIC-Bsa4
 * -- at appointed times
 * In order to make lots of plasmid that we will need for cloning:
 * -- Plasmid Midi-prep (in pairs) - use Tony's new protocol
 * Design Tail Primers for targets, order tail primers

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall14.doc

PyMol Refresher due for Springers (plus Zain and Hailey) can count as 2 hours of lab time
 * 22-SepMonday**
 * 23-SepTuesday**
 * 24-SepWednesday**
 * 25-SepThursday**


 * 26-SepFriday**
 * 27-SepSaturday**
 * 28-SepSunday**

Target page updates due - 9 pm || **WEEK5**


 * Wet Lab**
 * continue cloning, expression, purification, storage
 * look up your substrates and how to order them
 * look up enzyme assay in other research papers

>> Protocol_LigandPrep_VDS_v1_?.docx >> ProtocolVirtualScreenYOURTarget_VDS_??.doc You don't have to do all of these protocols right away - but you should aim to have your Homology model created this week and have started on Control Ligands selection (the first part of the Virtual Screening Protocol). -- see the sign up spreadsheet above for times
 * Virtual Work**
 * Begin Virtual Screening setup (see meeting times)
 * create homology model if needed for your target
 * ProtocolHomologyModelVDS_v?.doc

Target Page - update yours with your team (the person who comes first on the list of names is the point person and delegates the work)

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTarget_VDS_Fall14.d

Virtual Screening Refresher due for Vets can count as 2 hours of lab time (Zain & Hailey) do PyMol Refresher
 * 22-SepMonday**
 * 23-SepTuesday**
 * 24-SepWednesday**


 * 25-SepThursday**
 * 26-SepFriday**
 * 27-SepSaturday**
 * 28-SepSunday**

Target page updates due - 9 pm || LINK TO EDIT THE PAGE: __Add your name__ to the time you want
 * **SIGN UP FOR SPRINGERS FOR 1st Lab Times:**

media type="custom" key="26483506" ||  ||
 * **WEEK6**

Check the Mentor schedule to see when mentors will be present in lab to help you out.


 * Wet Lab**
 * Design Tail Primers for targets, order tail primers
 * ProtocolPCR_PrimerDesignTails_for_pNIC-Bsa4CloningFall14.doc
 * Primary PCR trials
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx
 * Midi-Prep your spun down pNIC-Bsa4
 * -- at appointed times (sign up on spreadsheet)
 * In order to make lots of plasmid that we will need for cloning:
 * -- Plasmid Midi-prep (**in pairs**) - use Tony's new protocol
 * Secondary PCR trials

Virtual Screening Refresher - start looking at will be due next week
 * Virtual Work**


 * 29-SepMonday**
 * Design Tail Primers for targets, order tail primers (sign up for times)


 * 30-SepTuesday**
 * Design Tail Primers for targets, order tail primers


 * 1-Oct Wednesday**
 * 2-Oct Thursday**
 * 3-Oct Friday**
 * 4-Oct Saturday**

__Mid Semester Research Report__ due (a.k.a. Report on your Target) Guidelines posted to: GDocs/__Results&Data__/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc || **WEEK6**
 * 5-Oct Sunday**
 * Cloning should be completed by end or September**
 * Start Expression**


 * Virtual Work**
 * Control Ligands selection and LigPrep is due at end of week
 * Beginning of the **ProtocolVirtualScreenYOURTarget_VDS_Fall14.doc**
 * Protocol_LigandPrep_VDS_v1_6.docx


 * 29-SepMonday**
 * 30-SepTuesday**
 * 1-Oct Wednesday**
 * 2-Oct Thursday**
 * 3-Oct Friday**
 * 4-Oct Saturday**
 * Lab Notebook check** - Saturdays at 5pm

__Mid Semester Research Report__ due (a.k.a. Report on your Target) Guidelines posted to: GDocs/__Results&Data__/ResearchReport/GuidelinesResearchReportonTarget_VDS_Fall14.doc ||
 * 5-Oct Sunday**
 * **WEEK7**

Check the Mentor schedule to see when mentors will be present in lab to help you out.

> WithQ5Polymerase_VDS_Fall14.docx > Secondary PCR trials
 * Wet Lab**
 * Primary PCR trials
 * ProtocolPCR_PrimerOverlap
 * Primer Dilution of your own tail primers

Virtual Screening Refresher - due in 2 weeks from now
 * Virtual Work**


 * 6-Oct Monday**
 * 7-Oct Tuesday**
 * 8-Oct Wednesday**
 * 9-Oct Thursday**
 * 10-OctFriday**
 * 11-OctSaturday**
 * Lab Notebook check** - Saturdays at 5pm


 * 12-OctSunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 5,6,7)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y&Z'** || **WEEK7**

- e.g homology model (if needed) and setting up protein in GOLD
 * Virtual Work**
 * Control Ligands selection and LigPrep is due at end of week
 * Beginning of the **ProtocolVirtualScreenYOURTarget_VDS_Fall14.doc**
 * Protocol_LigandPrep_VDS_v1_6.docx
 * Virtual Set up is due at end of week
 * Submit docking job of control ligands is due at end of week
 * ProtocolHomologyModelVDS_v5.doc

- analyze control ligands' scores

We will set up


 * 6-Oct Monday**
 * 7-Oct Tuesday**
 * 8-Oct Wednesday**
 * 9-Oct Thursday**
 * 10-OctFriday**
 * 11-OctSaturday**
 * Lab Notebook check** - Saturdays at 5pm


 * 12-OctSunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 5,6,7)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y&Z'** ||
 * **WEEK8**

Check the Mentor schedule to see when mentors will be present in lab to help you out. We will also have some dedicated virtual screening help sessions (see below)

* Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)
 * Wet Lab**
 * continue cloning work on your project
 * start cutting your pNIC-Bsa4 while working on your PCRs
 * Virtual Work**

5-7 pm Virtual Screening Help Session in wet lab 3-7 pm Virtual Screening Help Session in wet lab
 * 13-OctMonday**
 * 14-OctTuesday**
 * 15-OctWednesday**

4-7 pm Help Session for: Virtual Screening & LICpNIC-Bsa4cloningExercise
 * 16-OctThursday**

2-6 PM Help Session for: Virtual Screening & LICpNIC-Bsa4cloningExercise
 * 17-OctFriday**

1- 4 PM Help Session for: Virtual Screening & LICpNIC-Bsa4cloningExercise
 * 18-OctSaturday**

Run1 of Virtual Screen Refresher due today LICpNIC-Bsa4cloningExerciseVDS_Fall14 due today


 * 19-OctSunday** || **WEEK8**


 * Wet Lab**
 * protein expressions
 * purchase your substrates with Dr. B
 * enzyme assays

- analyze control ligands' scores - submit jobs for small screening libraries (cb306, NIHcc) ---InHouseCompounds (~40 ligs) -use 1 processor ---CB306 (306 ligs) - use 1 processor ---NIHClinicalCollection (446 ligs), use 1 processor ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
 * Virtual Work**

--- If those look good - submit CBDiversity (large library - ~50k)


 * 13-OctMonday**
 * 14-OctTuesday**
 * 15-OctWednesday**
 * 16-OctThursday**
 * 17-OctFriday**


 * 18-OctSaturday**


 * 19-OctSunday** ||
 * **WEEK9**

Check the Mentor schedule to see when mentors will be present in lab to help you out. We will also have some dedicated virtual screening help sessions (see below)


 * Wet Lab**
 * continue cloning work on your project
 * start cutting your pNIC-Bsa4 while working on your PCRs
 * once PCR Squared is done - carry out cloning protocol
 * ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
 * make sucrose + kan plates if there aren't any (get a mentors help)
 * Virtual Work**

* Virtual Screening Refresher (can count as 4 hrs of wet lab time for the whole exercise)


 * 20-OctMonday**

Virtual Screening Refresher - due
 * 21-OctTuesday**
 * 22-OctWednesday**
 * 23-OctThursday**
 * 24-OctFriday**
 * 25-OctSaturday**


 * 26-OctSunday**

Peer Review of Mid Semester Research Report on target --- see GDrive folder for instructions ( ResearchReport_Materials&Methods_Guidelines) || **WEEK9**


 * Wet Lab**
 * purchase your substrates with Dr. B (if you have not already done so)
 * enzyme assays - does your enzyme work?

- analyze scores - submit jobs for a large screening library (CB Diversity - 50k)
 * Virtual Work**
 * only use ~ 6 processors so that everyone can run their jobs


 * 20-OctMonday**


 * 21-OctTuesday**
 * 22-OctWednesday**
 * 23-OctThursday**
 * 24-OctFriday**
 * 25-OctSaturday**
 * 26-OctSunday**

Peer Review of Mid Semester Research Report on target --- see GDrive folder for instructions ( ResearchReport_Materials&Methods_Guidelines) ||
 * **WEEK10**

Check the Mentor schedule to see when mentors will be present in lab to help you out. We will also have some dedicated virtual screening help sessions (see below)


 * Wet Lab**
 * continue cloning work on your project
 * carry out cloning protocol
 * ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
 * make sucrose + kan plates if there aren't any (get a mentors help)


 * Virtual Work**
 * Control Ligands selection and LigPrep
 * Virtual Set up
 * Submit docking job of control ligands

Lab Notebook Due at 5pm
 * 27-OctMonday**
 * 28-OctTuesday**
 * 29-OctWednesday** - Journal Club
 * 30-OctThursday**
 * 31-OctFriday**
 * 1-Nov Saturday**


 * 2-Nov Sunday**

Cloning Materials & Methods due

Wikispaces posting due - Sundays at 9 pm **(For Weeks 8,9,10)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week 8, 9, and 10'** || **WEEK10**

- ChemBridge Diversity Priority: Luis, Charina, Andee, Nikki, Andrei, Hailey
 * Enzyme Assays**
 * Virtual Screening**

Lab Notebook Due at 5pm
 * 27-OctMonday**
 * 28-OctTuesday**
 * 29-OctWednesday** - Journal Club
 * 30-OctThursday**
 * 31-OctFriday**
 * 1-Nov Saturday**


 * 2-Nov Sunday**

Cloning Materials & Methods due

Wikispaces posting due - Sundays at 9 pm **(For Weeks 8,9,10)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week 8, 9, and 10'** ||
 * **WEEK11**

Check the Mentor schedule to see when mentors will be present in lab to help you out. We will also have some dedicated virtual screening help sessions (see below)


 * Wet Lab**
 * continue cloning work on your project
 * carry out cloning protocol
 * ProtocolpNIC-Bsa4_cloningVDS_Fall14.doc
 * make sucrose + kan plates if there aren't any (get a mentors help)


 * Virtual Work**
 * Control Ligands selection
 * ProtocolVirtualScreenYOURTarget_VDS_??.doc (first part only for now = Control Ligand Selection)


 * 3-Nov Monday**
 * 4-Nov Tuesday**
 * 5-Nov Wednesday**
 * 6-Nov Thursday**
 * 7-Nov Friday**
 * 8-Nov Saturday**
 * 9-Nov Sunday**

Peer Review of M&M Cloning Due at m/n - –You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB || **WEEK11**


 * Enzyme Assays**


 * 3-Nov Monday**


 * 4-Nov Tuesday**
 * 5-Nov Wednesday**
 * 6-Nov Thursday**
 * 7-Nov Friday**
 * 8-Nov Saturday**
 * 9-Nov Sunday**

Peer Review of M&M Cloning Due at m/n –You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB ||
 * **WEEK12**


 * Virtual Work**
 * Control Ligands - LigPrep
 * Protocol_LigandPrep_VDS_v1.docx
 * Virtual Set up
 * ProtocolVirtualScreenYOURTarget_VDS.doc
 * create homology model if needed for your target
 * ProtocolHomologyModelVDS_v.doc
 * Submit docking job of control ligands


 * Virtual Work**
 * - analyze control ligands' scores
 * - submit jobs for small screening libraries (cb306, NIHcc, HF9)
 * ---InHouseCompounds (~40 ligs) -use 1 processor
 * ---CB306 (306 ligs) - use 1 processor
 * ---NIHClinicalCollection (446 ligs), use 1 processor
 * ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor

no journal club this week Virtual M&M due || **Enzyme Assays**
 * 10-NovMonday**
 * 11-NovTuesday**
 * 12-NovWednesday**
 * 13-Nov Thursday**
 * 14-Nov Friday**
 * 15-NovSaturday**
 * 16-NovSunday**
 * determine is your enzyme is active
 * determine how much enzyme to use to get 'good' absorbance signal
 * vary amount of substrates(s) to optimize assay


 * Virtual Work**
 * - analyze control ligands' scores
 * - submit jobs for small screening libraries (cb306, NIHcc, HF9)
 * ---InHouseCompounds (~40 ligs) -use 1 processor
 * ---CB306 (306 ligs) - use 1 processor
 * ---NIHClinicalCollection (446 ligs), use 1 processor
 * ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
 * --- If those look good - submit CBDiversity (large library - ~50k)

no journal club this week Virtual M&M due ||
 * WEEK12**
 * 10-NovMonday**
 * 11-NovTuesday**
 * 12-NovWednesday**
 * 13-Nov Thursday**
 * 14-Nov Friday**
 * 15-NovSaturday**
 * 16-NovSunday**
 * **WEEK13**

Journal Club
 * Virtual Work**
 * - analyze scores
 * - continue screening small screening libraries (cb306, NIHcc, HF9)
 * ---InHouseCompounds (~40 ligs) -use 1 processor
 * ---CB306 (306 ligs) - use 1 processor
 * ---NIHClinicalCollection (446 ligs), use 1 processor
 * ---HF9PlatesPlates5_9.sdf (400 ligs) - use 1 processor
 * 17-Nov Monday**
 * 18-Nov Tuesday**
 * 19-Nov Wednesday**
 * 19-Nov Wednesday**

Lab Notebook Due at 5pm
 * 20-Nov Thursday**
 * 21-Nov Friday**
 * 22-Nov Saturday**


 * 23-Nov Sunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 11,12,13)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y&Z'** || **WEEK13**


 * Enzyme Assays & Inhibition Assays**
 * determine if your enzyme is active
 * determine how much enzyme to use to get 'good' absorbance signal
 * vary amount of substrates(s) to optimize assay
 * Dilute inhibitors in DMSO
 * test out inhibitors (vary concentration)


 * Virtual Work**
 * - analyze scores for ChemBridge Diversity

Journal Club
 * 17-Nov Monday**
 * 18-Nov Tuesday**
 * 19-Nov Wednesday**

Lab Notebook Due at 5pm
 * 20-Nov Thursday**
 * 21-Nov Friday**
 * 22-Nov Saturday**


 * 23-Nov Sunday**

Wikispaces posting due - Sundays at 9 pm **(For Weeks 11,12,13)** Add content to YOUR __research__ page on Wikispaces Put a line and **'Week X&Y&Z'** || do some virtual screening
 * **Virtual Work**

we will have mentors on duty for Mon, Tues, Wed - so continue your cloning work if you are in town
 * Wet Lab work**


 * WEEK14**
 * 24-Nov Monday**

Peer Review of M&M Virtual Due at m/n –You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB
 * 25-Nov Tuesday -**

Expression, Purification, Characterization M&M due (can also turn in on Sunday night (Nov 30th)
 * It may be part of your proposed methods – but it still must be detailed.
 * I want you to think about the process and be able to explain the concepts.
 * You have done a somewhat similar Expression, Purification & Characterization in spring

We will have mentors on duty if you want to do lab work
 * 26-Nov Wednesday - NO CLASS (Thanksgiving Break)**

see above for Peer Review and M&M that are due || **Virtual Work** do some virtual screening
 * 27-Nov Thursday**
 * 28-Nov Friday**
 * 29-Nov Saturday**
 * 30-Nov Sunday**

we will have mentors on duty for Mon, Tues, Wed
 * Wet Lab work**


 * WEEK14**
 * 24-Nov Monday**

Peer Review of M&M Virtual Due at m/n – You have 2 different people’s which you need to review –Make 5 constructive criticisms –Make 2 compliments - make sure to add your Initials to each comment so we know who did what - JTB
 * 25-Nov Tuesday**

Expression, Purification, Characterization M&M due (can also turn in on Sunday night (Nov 30th)

We will have mentors on duty if you want to do lab work
 * 26-Nov Wednesday - NO CLASS (Thanksgiving Break)**

see above for Peer Review and M&M that are due ||
 * 27-Nov Thursday**
 * 28-Nov Friday**
 * 29-Nov Saturday**
 * 30-Nov Sunday**