Timeline+F12

=TIMELINE FOR RESEARCH= Schedule of things we will do over the semester NOTE - see middle 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
 * Researcher's Names**:
 * Summer **Veterans**: Aldo, Andrew, Michael, Daniel, Janice, Max, Urvashi, Alex, Kaarthik, Aakash,
 * **Sidestreamers**: Akhilesh, Rishi, Paul, Priya, Vanna, Keyur, Ben, Jennifer
 * **Springers**: Shane, Suman, Stephanie, Divya, Brandon, Ivy, Sajan, Tom, Mihir, Rufei, Ling


 * ===** This Week **=== || ===** This Week **=== ||
 * ** SPRINGERS ** || ** VETERANS ** ||
 * **ITEMS FOR THE WEEK:**

__Enzyme assays__ with your surrogate enzyme: //ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx//

__Start Inhibition assays__. //ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx// Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)

__Finish Virtual Screening__

cb306 and CBkinUT

LAST VDS CLASS
 * 3-Dec Monday**
 * 4-Dec Tuesday**
 * 5-Dec Wednesday**

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

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/

Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
 * 6-Dec Thursday**

Lab Cleanup
 * 7-Dec Friday**

Final Lab Report Due Final LAB NOTEBOOK CHECK
 * 8-Dec Saturday**


 * 9-Dec Sunday** || **ITEMS FOR THE WEEK:**

continue with wet lab work

Start Inhibition assays. Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)

Analyze **and post your** library screening results to GDocs

LAST VDS CLASS
 * 3-Dec Monday**
 * 4-Dec Tuesday**
 * 5-Dec Wednesday**

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

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/

Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
 * 6-Dec Thursday**

Lab Cleanup
 * 7-Dec Friday**

Final Lab Report Due Final LAB NOTEBOOK CHECK
 * 8-Dec Saturday**


 * 9-Dec Sunday** ||
 * ===** Next Week **=== || ===** Next Week **=== ||
 * ** SPRINGERS ** ||= VETERANS ||
 * **ITEMS FOR THE WEEK:** || **ITEMS FOR THE WEEK:** ||
 * Dr. B Notes ||  ||
 * Enzyme Assay kinetics lab (phosphatase)
 * Dr. B Notes ||  ||
 * Enzyme Assay kinetics lab (phosphatase)
 * Dr. B Notes ||  ||
 * Enzyme Assay kinetics lab (phosphatase)

Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall12.doc ProtocolProteinPurificationVDS_Fall12.doc ProtocolHomemadeSDSPageGelSolutionsVDS_Fall12.docx - Skip this one (the Mentors will make gels for you) ProtocolProteinCharacterizationVDS_Fall12.doc ProtocolFPLC_GelFiltration_VDS_Fall12.docx ProtocolLabEnzymeTest_Phosphatase_VDS_Fall12.xlsx Enzyme Assays on target Inhibition Assays on target Optional: VINA tutorial BASH or Perl script || Comparison Dock (ICM, GOLD, VINA) ||
 * **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** || **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** ||
 * **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** || **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** ||
 * **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** || **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** ||
 * 15-DecSaturday**
 * 16-DecSunday** || **10-DecMonday**
 * 11-DecTuesday**
 * 12-DecWednesday**
 * 13-DecThursday**
 * 14-DecFriday**
 * 15-DecSaturday**
 * 16-DecSunday** ||

PAST DATE

Target Discovery Target Discovery - order primers
 * **Springers** || **Veterans** ||
 * GENERAL ITEMS FOR THE WEEK:

DATE-SPECIFIC ITEMS
 * 27-Aug Monday**


 * 28-Aug Tuesday**

2 - 3pm - **Lab Group Meeting** - RLM 11.176
 * 29-Aug Wednesday**

Create a GDocs folder in /StudentFolders - FirstnameLastInitial (e.g. WilliamB) Create a Wikispaces page under Research Pages

3:30 - 6pm - Target Discovery Session in WEL 2.114 --Pick new target


 * 30-Aug Thursday**

Target Discovery Session (1-5 pm in WEL 2.114) --Pick new target
 * Design Overlap Primers ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall12.doc
 * - post final primers to Wikispaces page


 * 31-Aug Friday**

ORDER Primers for you target PRIMER ORDERING SESSION: 1 - 4:30 in WEL 2.114 - Comp Lab

Spreadsheet for ordering primers is at: Google Docs/VDS/Misc/Primers/**PrimerPlateOrderTemplate_GDocs_AugFall_2012**

Wikispaces check on each Friday Your WikiPage should have: been created by now, brief detail of what you have done these last 3 days

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

submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev) -- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc


 * 1-Sep Saturday**
 * 2-Sep Sunday**

Download & print needed protocols from GDocs -- under /**Protocols/Cloning/FirstProtocols** Submit to DNA Sequencing -- in 2 days retrieve and save results to your GDocs folder RE Digest -- save results to your GDocs folder -- post image commentary to your Wikispace page

Analyze DNA sequence exercise Virtual Screening Refresher || Finish cloning your gene into pNIC-Bsa4 Transform positive clone with your gene into BL21(De3) cells - begin expression PyMol Refresher - Due by ?? Science Works assignment due ??


 * 27-Aug Monday**


 * 28-Aug Tuesday**

2 - 3pm - **Lab Group Meeting**/Journal Club (in ???? classroom)
 * 29-Aug Wednesday**


 * 30-Aug Thursday**


 * 31-Aug Friday**

PyMol Refresher - due next Wed Wikispaces check on each Friday

-- in 2 days retrieve and save results to your GDocs folder RE Digest -- save results to your GDocs folder -- post image commentary to your Wikispace page
 * 1-Sep Saturday**
 * 2-Sep Sunday** ||
 * Submit to DNA Sequencing

12 - 4 pm Target Discovery & Primer Design & Primer ordering
 * 3-Sep Monday**

Spreadsheet for ordering primers is at: Google Docs/VDS/Misc/Primers/**PrimerPlateOrderTemplate_GDocs_AugFall_2012**

If your primers have been uploaded: ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev) -- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev) ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
 * 4-Sep Tuesday**

Target Discovery

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

2 - 3pm - **Lab Group Meeting** (in **RLM 11.176** classroom)
 * 5-Sep Wednesday**

ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev) (~1.5 hrs) -- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev) ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc

Transformation of pNIC-Bsa4 in Dh5alpha (~2-2.5 hrs)

Retrieve results on line from DNA Sequencing core website for your results from: -- "**Submit to DNA Sequencing**" - save results to your GDocs folder
 * 6-Sep Thursday**

RE digest & Agarose Gel - of pGBR22 --- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break) --- ProtocolNanoDropVDS.doc (~2hrs)

Transformation of pNIC-Bsa4 in Dh5alpha


 * 7-Sep Friday**

Springers - Finish up your **Target page** that you created in Target Discovery Protocol, even if it was not one that was chosen. This will be for a grade.

3:30 - 6:30 Analyze DNA sequence exercise (in WELCH computer lab) -- save the assignment as WORD doc to your GDocs folder

Wikispaces check on each Friday Your WikiPage should have
 * images of all PCR gels (well annotated - i.e. descriptions and what each lane is)
 * image of RE digest gel (well annotated)
 * Paste a copy of your DNA sequence from the DNA sequencing core (briefly describe what it is)


 * 8-Sep Saturday**
 * 9-Sep Sunday** || **3-Sep Monday**
 * Help Sessions: PyMol and Virtual Screen Refresher Welch Computer Lab
 * 4-Sep Tuesday**
 * 4-Sep Tuesday**

2 - 3pm - **Lab Group Meeting** (in **RLM 11.176** classroom) PyMol Refresher - due today
 * 5-Sep Wednesday**


 * 6-Sep Thursday**


 * 7-Sep Friday**

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!

--- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break) --- ProtocolNanoDropVDS.doc (~2hrs)
 * 8-Sep Saturday**
 * 9-Sep Sunday** ||
 * 1. RE digest & Agarose Gel - of pGBR22

2. Retrieve results on line from DNA Sequencing core website for your results from: -- "**Submit to DNA Sequencing**" - save results to your GDocs folder

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


 * 3. Grow up pNIC_bsa4 in DH5alpha o/n in 1x160ml - store pellets**


 * 4. Midi prep pNIC-Bsa4 (later in week - Th or Fri in groups)**


 * 5.** Practice PCR #1: **ProtocolPCRVDS.xls** with TAQ poly

2 - 3pm - **Lab Group Meeting**(in NEW classroom: **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 10-SepMonday**
 * 11-SepTuesday**
 * 12-SepWednesday**

Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm
 * 13-SepThursday**
 * 14-SepFriday --FRI Picnic (Mentors & Dr. B)**
 * all protocols (PCR, RE Digest, analyze DNA, submit DNA)
 * all gel images
 * Analyze DNA Sequence exercise work
 * Protocol, Order form and Results from ProtocolDNASequencingFacilityVDS_Fall11.doc


 * 15-SepSaturday**
 * 16-SepSunday -** Wikispaces check on each Sunday night by 9:00 pm || clone your gene!

New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik ---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx

Virtual Screen Refresher - due next week (Friday Sept 22nd)

2 - 3pm - **Lab Group Meeting**(in NEW classroom: **RLM 10.176**) - includes JOURNAL CLUB*
 * 10-SepMonday**
 * 11-SepTuesday**
 * 12-SepWednesday**


 * 13-SepThursday**
 * 14-SepFriday**
 * --5-7pm FRI Picnic (Mentors & Dr. B)**

Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm


 * 15-SepSaturday**
 * 16-SepSunday -** Wikispaces check on each Sunday night by 9:00 pm ||
 * **ITEMS FOR THE WEEK:**
 * Should have already completed: RE digest, Nanodrop, Submit to DNA, Analyze DNA, Transformation, etc.**

(**NOTE**: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet - in /Misc/PlasmidConcentrations . ONLY a few of you have uploaded yours.


 * Midi prep pNIC-Bsa4
 * Practice PCR #1: **ProtocolPCRVDS.xls**with TAQ poly
 * this PCR must work correctly before you can proceed
 * Practice PCR #2: **ProtocolPCR_pLICsequencing.xls** on pNIC-Bsa4 with Taq poly using pLicFor and pLicRev

2 - 3pm - **Lab Group Meeting**(in NEW classroom: **RLM 10.176**)
 * 17-SepMonday**
 * 18-SepTuesday**
 * 19-SepWednesday -**


 * 20-SepThursday**
 * 21-SepFriday** ? FRI Picnic (Mentors & Dr. B)??
 * 22-SepSaturday**
 * 23-SepSunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || **ITEMS FOR THE WEEK:**
 * Continue cloning**


 * Virtual Screen Refresher - due (Friday Sept 22nd)**

2 - 3pm - **Lab Group Meeting**(in NEW classroom: **RLM 10.176**)
 * 17-SepMonday**
 * 18-SepTuesday**
 * 19-SepWednesday**

- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
 * 20-SepThursday**
 * 21-SepFriday** ? FRI Picnic (Mentors & Dr. B)??
 * 22-SepSaturday**
 * 23-SepSunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * (**NOTE**: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
 * Practice PCR #2: **ProtocolPCR_pLICsequencing.xls** on pNIC-Bsa4 with Taq poly using pLicFor and pLicRev

Design Tail Primers **ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc -**
 * this is a priority - Dr. B has to check it before we can order them
 * - post final primers __to Wikispaces page__

ProtocolPCR_PrimerOverlapVDS _fall12.docx - 1st step is to __Make Oligo Mix__ (takes an hour or two)

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 24-SepMonday**
 * 25-SepTuesday**
 * 26-SepWednesday**


 * 27-SepThursday**
 * 28-SepFriday**

PyMol refresher due date changed to this Saturday Sept 29th
 * 29-SepSaturday**

-- PyMol refresher due date changed again to this Sunday Sept 30th - i would rather you focus on your ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc || **24-SepMonday** 2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 30-SepSunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm
 * 25-SepTuesday**
 * 26-SepWednesday**

-- 1st step: Make Oligo Mix -- 2nd step: Primary PCR -- 3rd step: Secondary PCR - need your custom 'tail' primers for this
 * 27-SepThursday**
 * 28-SepFriday**
 * 29-SepSaturday**
 * 30-SepSunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * ProtocolPCR_PrimerOverlapVDS_Fall12.docx

-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest -- takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)

-- Clone your gene into accepting vector -ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc

Design Tail Primers **ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc -**
 * 1-Oct Monday**
 * this is a priority - Dr. B has to check it before we can order them
 * - post final primers __to Wikispaces page__

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**)
 * 2-Oct Tuesday**
 * 3-Oct Wednesday**


 * 4-Oct Thursday**
 * 5-Oct Friday**
 * 6-Oct Saturday**
 * 7-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm

(**NOTE**: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet - in /Misc/PlasmidConcentrations . ONLY a few of you have uploaded yours. || **ITEMS FOR THE WEEK:**

Should be getting closer to finishing cloning

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**)
 * 1-Oct Monday**
 * 2-Oct Tuesday**
 * 3-Oct Wednesday**


 * 4-Oct Thursday**
 * 5-Oct Friday**
 * 6-Oct Saturday**
 * 7-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * ProtocolPCR_PrimerOverlapVDS_Fall12.docx

-- 2nd step: Primary PCR -- 3rd step: Secondary PCR - need your custom 'tail' primers for this

-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest -- takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)

-- Clone your gene into accepting vector
 * **ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc**

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 8-Oct Monday**
 * 9-Oct Tuesday**
 * 10-Oct Wednesday**


 * 11-Oct Thursday**
 * 12-Oct Friday**
 * 13-Oct Saturday**
 * 14-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || Should be finishing cloning


 * 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

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 8-Oct Monday**
 * 9-Oct Tuesday**
 * 10-Oct Wednesday**


 * 11-Oct Thursday**
 * 12-Oct Friday**
 * 13-Oct Saturday**
 * 14-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * **-- Clone your gene into accepting vector**
 * ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc

Virtual Screen Refresher - changed due date to tomorrow
 * 15-Oct Monday**
 * 16-Oct Tuesday**

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 17-Oct Wednesday**

Virtual Screen Refresher - **due at midnight (Wed)**

LAB NOTEBOOK CHECK
 * 18-Oct Thursday**
 * 19-Oct Friday**

- Wikispaces check on each Sunday night by 9:00 pm || **Finish cloning**
 * 20-Oct Saturday**
 * 21-Oct Sunday**

Check sequence, grow up large amount for Midi-prep

Transform into BL21(DE3) cells


 * Continue Virtual Screening of your target**

-- the sooner this is done, the faster we can order compounds


 * ProtocolHomologyModelVDS_v3.doc
 * ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
 * ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
 * Protocol_ICM_VDSv1_3.docx

2 - 3pm - **Lab Group Meeting**(in : **RLM 10.176**) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 15-Oct Monday**
 * 16-Oct Tuesday**
 * 17-Oct Wednesday**

LAB NOTEBOOK CHECK
 * 18-Oct Thursday**
 * 19-Oct Friday**


 * 20-Oct Saturday**
 * 21-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * **-- Clone your gene into accepting vector**
 * ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc

Begin **Virtual Screening Protocols** for your real target - not practice!

in GDOCS **/Protocols/VirtualScreeningProtocols/**


 * ProtocolHomologyModelVDS_v3.doc (if necessary)
 * ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
 * ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
 * Protocol_ICM_VDSv1_3.docx

Research Report on Target Due @ midnight PyMol Image Contest
 * 22-Oct Monday**
 * 23-Oct Tuesday**
 * 24-Oct Wednesday**
 * 25-Oct Thursday**
 * 26-Oct Friday**
 * 27-Oct Saturday**
 * 28-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || **Finish cloning**

Check sequence, grow up large amount for Midi-prep

Transform into BL21(DE3) cells


 * Continue Virtual Screening of your target**

-- the sooner this is done, the faster we can order compounds

Research Report on Target Due @ midnight PyMol Image Contest
 * ProtocolHomologyModelVDS_v3.doc
 * ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
 * ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
 * Protocol_ICM_VDSv1_3.docx
 * 22-Oct Monday**
 * 23-Oct Tuesday**
 * 23-Oct Tuesday**
 * 24-Oct Wednesday**
 * 25-Oct Thursday**
 * 26-Oct Friday**
 * 27-Oct Saturday**
 * 28-Oct Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * **-- Clone your gene into accepting vector**
 * ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc

Your protein should be setup for **GOLD** screening by this week and **CB306** library screened

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 29-OctMonday**
 * 30-OctTuesday**
 * 31-OctWednesday**
 * 1-Nov Thursday - Dr. B out of town**


 * 2-Nov Friday - Dr. B out of town**
 * 3-Nov Saturday - Dr. B out of town**
 * 4-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || Your protein should be setup for **GOLD** screening by this week

and **CB306** library screened and analyzed and **ChembridgeDiversity** library should be started

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 29-OctMonday**
 * 30-OctTuesday**
 * 31-OctWednesday**
 * 1-Nov Thursday - Dr. B out of town**
 * 2-Nov Friday - Dr. B out of town**
 * 3-Nov Saturday - Dr. B out of town**
 * 4-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * Finish cloning
 * Finish cloning

OR

Start screening **ChembridgeDiversity** library

Cloning Materials & Methods due
 * 5-Nov Monday**
 * 6-Nov Tuesday**

Cloning Materials & Methods due
 * 7-Nov Wednesday**
 * 8-Nov Thursday**


 * 9-Nov Friday**
 * 10-NovSaturday**
 * 11-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || Continue with cloning and/or protein expression

Analyze both **CB306 and** **ChembridgeDiversity** library results

Create a **TopLigands** (protocol in GDocs) list and manually enter the Top 5 to the Google Docs spreadsheet

Cloning Materials & Methods due
 * 5-Nov Monday**
 * 6-Nov Tuesday**

Cloning Materials & Methods due
 * 7-Nov Wednesday**
 * 8-Nov Thursday**

Analyze your **CB306** library screening results Start **CBKin-UT library.** (4,000 ligands)
 * 9-Nov Friday**
 * 10-NovSaturday**
 * 11-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * Continue expressing, purifying your surrogate enzyme


 * 12-Nov Monday**
 * 13-Nov Tuesday**

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 14-Nov Wednesday**

LAB NOTEBOOK CHECk
 * 15-Nov Thursday**
 * 16-Nov Friday**


 * 17-Nov Saturday**

Virtual M&M due - Sunday at 9 pm. see **VDSFall12_Guide_M&M_Virtual_VDS.docx** in Google Docs
 * 18-Nov Sunday**

OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
 * -** Wikispaces check on each Sunday night by 9:00 pm || Analyze **and post your** library screening results to GDocs


 * 12-Nov Monday**
 * 13-Nov Tuesday**

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 14-Nov Wednesday**

LAB NOTEBOOK CHECK
 * 15-Nov Thursday**
 * 16-Nov Friday**

Virtual M&M due - Sunday at 9 pm. see **VDSFall12_Guide_M&M_Virtual_VDS.docx** in Google Docs
 * 17-Nov Saturday**
 * 18-Nov Sunday**

Analyze your **CB306** library screening results Start **CBKin-UT library.** (4,000 ligands)
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * Continue purifying and characterizing your surrogate enzyme

5-6 pm - **Lab Group Meeting**(in : RLM 12.166) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 19-Nov Monday**


 * 20-Nov Tuesday**
 * 21-Nov Wednesday**
 * 22-Nov Thursday**

OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
 * 23-Nov Friday**
 * 24-Nov Saturday**
 * 25-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm || Analyze **and post your** library screening results to GDocs

5-6 pm - **Lab Group Meeting**(in : RLM 12.166) - includes JOURNAL CLUB* -- read the article at least 2 times and answer questions to turn in at start of class -- bring a PAPER copy of article with you for Discussion
 * 19-Nov Monday**


 * 20-Nov Tuesday**
 * 21-Nov Wednesday**
 * 22-Nov Thursday**

//ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx//
 * 23-Nov Friday**
 * 24-Nov Saturday**
 * 25-Nov Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||
 * __Enzyme assays__ with your surrogate enzyme:

__Start Inhibition assays__. //ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx// Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)

Analyze your **CB306** library & **CBKin-UT** library screening results
 * post your** TopLigands to GDocs (Ignore ICM work)

26-Nov Monday 27-Nov Tuesday Expression M&M due
 * VDSFall12_Guide_M&M_ExpressionPurification_VDS.docx** in Google Docs

28-Nov Wednesday 2 - 3pm - Lab Group Meeting(in : RLM 10.176) no journal club

29-Nov Thursday 30-Nov Friday 1-Dec Saturday 2-Dec Sunday - Wikispaces check on each Sunday night by 9:00 pm || continue with wet lab work

Start Inhibition assays (if you have protein). Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)

Analyze **and post your**library screening results to GDocs (Ignore ICM work) OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds

Expression M&M due
 * 26-Nov Monday**
 * 27-Nov Tuesday**
 * VDSFall12_Guide_M&M_ExpressionPurification_VDS.docx** in Google Docs

2 - 3pm - **Lab Group Meeting**(in : RLM 10.176) no journal club
 * 28-Nov Wednesday**


 * 29-Nov Thursday**
 * 30-Nov Friday**
 * 1-Dec Saturday**
 * 2-Dec Sunday**
 * -** Wikispaces check on each Sunday night by 9:00 pm ||

FROM FALL 11


 * 1st Week (8/31 – 9/2) **


 * 2nd Week (9/5 – 9/9) **

PyMol Refresher (see Announcement page for PyMol Help Session on Thursday 9/14)
 * 3rd Week (9/12 – 9/16) **
 * Due next week for Returning Spring VDSers
 * Due week after next for New VDSers (Joshua, Hong, Marshall, Shreya, Indra)

Once you have successfully completed first PCR,
 * Practice PCR: **ProtocolPCR_pLICsequencing.xls**
 * Then begin cloning
 * Design Overlap Primers **ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall11.doc**
 * Design Tail Primers **ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall11.doc**
 * Primary PCR with Oligo Mix **ProtocolPCR_PrimerOverlapVDS_Fall11.docx**
 * Secondary PCR w/ Tail primers **same**

Science Works assignment due Friday Sept 16th - see announcement page

Lab Notebook Check this Friday - leave your notebook in 'Drug Screening Notebooks' drawer in lab by 7:00 pm Wikispaces check on each Friday
 * all protocols (PCR, RE Digest, analyze DNA, submit DNA)
 * all gel images
 * Analyze DNA Sequence exercise work
 * Protocol, Order form and Results from ProtocolDNASequencingFacilityVDS_Fall11.doc

PyMol Refresher
 * 4th Week (9/19 – 9/23) **
 * Due Tues (9/20) for New VDSers (Joshua, Hong, Marshall, Shreya, Indra)
 * Help Sessions: PyMol and Virtual Screen Refresherin Welch Computer Lab
 * Monday Sept 19th: 5-7 pm


 * begin cloning
 * Design Overlap Primers **ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall11.doc**
 * Design Tail Primers **ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall11.doc**
 * Primary PCR with Oligo Mix **ProtocolPCR_PrimerOverlapVDS_Fall11.docx**
 * Secondary PCR w/ Tail primers **same**

Virtual Screen Refresher - due next week (Tues 9/27) Wikispaces check on each Friday

begin cloning
 * <span style="font-family: 'Times New Roman','serif';">Week 5 (9/26 – 9/30) **
 * Design Overlap Primers **ProtocolPCR_PrimerDesign_OverlapAssemblyVDS_Fall11.doc**
 * Design Tail Primers **ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall11.doc**
 * Primary PCR with Oligo Mix **ProtocolPCR_PrimerOverlapVDS_Fall11.docx**
 * Secondary PCR w/ Tail primers **same protocol**

For Virtual Refresher: Since the blades are full - you only need to have your first Run started by the end of this week. (by Friday 9/30)

VDSers that are returning from Spring:
 * Begin **real** Virtual Screening - prepare protein in GOLD and start jobs (cb306 should be done this week and the next one started)

Wikispaces check on each Friday

<span style="font-family: 'Times New Roman','serif';">Submit 2nd job of Virtual Screen Refresher <span style="font-family: 'Times New Roman','serif';">Begin Virtual Screening on YOUR target Virtual Screening
 * <span style="font-family: 'Times New Roman','serif';">Week 6 (10/3 – 10/7) **

Continue cloning
 * complete both primer design exercises
 * complete 1st and 2nd Overlap PCR

Wikispaces check on each Friday Target Selection exercise ?
 * Lab Notebook check this Friday** (7:00 pm)

10/03/11 - Still need PyMol Refresher from: **Michael E**., **Shutian J**., **Giancarlo M**., **Shreya N**., **Indra S**. , **Hong C.**

Journal Club 3 Research Report Due - Tues Oct. 11th - Guidelines in GDocs folder Continue **real** Virtual Screening - prepare protein in GOLD and start jobs >
 * <span style="font-family: 'Times New Roman','serif';">Week 7 (10/10 – 10/14) **
 * Virtual Screening help session for setting up your protein (should have 1st library done this week)
 * Monday 4 - 5:30 in WEL 2.306 Computer Lab.


 * 1) complete both primer design exercises
 * 2) complete 1st and 2nd Overlap PCR

PyMol Image contest Due Friday at Midnight

Wikispaces check on each Friday

verify positive clones with Wikispaces check on each Friday
 * <span style="font-family: 'Times New Roman','serif';">Week 8 (10/17 – 10/21) **
 * <span style="font-family: 'Times New Roman','serif';">VIRTUAL SCREENING - should have 3 libraries completed. **
 * <span style="font-family: 'Times New Roman','serif';">Perform cloning protocol on your target: **
 * ProtocolpNIC-Bsa4_cloningVDS_Fall11.doc
 * ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall11.doc

Journal Club 4 Express your enzyme or Sat night if working on Sat. Wikispaces check on each Friday
 * <span style="font-family: 'Times New Roman','serif';">Week 9 (10/24 – 10/28) **
 * <span style="font-family: 'Times New Roman','serif';">VIRTUAL SCREENING ** - finish by this week - do **Top Ligands Procotol** to get final compounds for ordering
 * Fri ( 10/28) Lab Notebook check this Friday**(7:00 pm)

Tues Nov. 1s t Thursday Nov 3rd at Midnight (Materials & Methods for **Cloning** due)
 * <span style="font-family: 'Times New Roman','serif';">Week 10 (10/31 – 11/4) **
 * <span style="font-family: 'Times New Roman','serif';">FRI External Open House - **<span style="font-family: 'Times New Roman','serif';">Wednesday Nov. 2nd 1- 4 pm

Express your enzyme Purify and Characterize your protein
 * Top Ligands Procotol** to get final compounds for ordering

Wikispaces check on each Friday

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

Journal Club 5 Tues Nov. 8th at Midnight (Materials & Methods for **Virtual Screening** due) - see Tips & Hints page Enzyme Assays Wikispaces check on each Friday
 * <span style="font-family: 'Times New Roman','serif';">Week 11 (11/7 – 11/11) **

Tues Nov. 15th at Midnight (Materials & Methods for **Expression, Purification, and Characterization** due) Purify and Characterize your protein - NOTE: this is a long and arduous process. Don't put it off. Enzyme Assays Inhibition Assays or Sat night if working on Sat. Wikispaces check on each Friday
 * <span style="font-family: 'Times New Roman','serif';">Week 12 (11/14 – 11/18) **
 * Fri ( 11/18) Lab Notebook check this Friday**(7:00 pm)

Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall11_ver2.doc ProtocolProteinPurificationVDS_Fall11.doc ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx - Skip this one (the Mentors will make gels for you) ProtocolProteinCharacterizationVDS_Fall11.doc ProtocolFPLC_GelFiltration_VDS_Fall11V_v2.docx

ProtocolLabEnzymeTest_Phosphatase_VDS_Fall11.xlsx Then on to Inhibition Assays once compounds arrive

Journal Club 6 Inhibition Assays - on 2 compounds Wikispaces check on each Friday
 * <span style="font-family: 'Times New Roman','serif';">Week 13 (11/21 – 11/25): Thanksgiving **

Inhibition Assays - on 2 compounds Tues Nov. 29th - __FINAL PRESENTATIONS of Enzyme Inhibition Graphs- everyone__ make a one slide PowerPoint and upload to the GroupMeetingSlides/FInalSlides_StudentsFall11 folder on GDocs save file with your name and date in the file name
 * <span style="font-family: 'Times New Roman','serif';">Week 14 (11/28 – 12/2) **


 * Thurs (12/1)** - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
 * Fri (12/2) -** Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)

Final Wikispaces check
 * Sat ( 12/3)**
 * Final Report due (5:00 pm )**
 * Final Lab Notebook check** (7:00 pm)