Timeline

TIMELINE FOR RESEARCH

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
 * 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)

PAPER COPY – Print out of TxClass Safety Training (can put in Safety section of VDS sign-in binder in lab)
 * 1st Week (8/31 – 9/2) **

Pick target from current list

TUES: (after class) Create a GDocs folder Create a Wikispaces page Analyze DNA sequence exercise (in WELCH computer lab) - save result to your GDocs folder

WED - FRI: - download protocols from GDocs under /**Protocols/Cloning/FirstProtocols** Submit to DNA Sequencing - save results to your GDocs folder RE Digest - save results to your GDocs folder and post image and commentary to your Wikispace page PCR - of pGBR22 - save results to your GDocs folder and post image and commentary to your Wikispace page


 * 2nd Week (9/5 – 9/9) **
 * 1) Print out of TxClass Safety Training -
 * PAPER COPY – put in Safety section of VDS sign-in binder in lab
 * 1) Check on line (DNA Sequencing core website) for your results from "**Submit to DNA Sequencing**" - save results to your GDocs folder
 * 2) Finish up PCR - this PCR must work correctly before you can proceed - Post final, properly labeled image to your Wikispaces page (Research Pages section) and, of course, in your labnoteook
 * 3) Finish up RE Digest - Post final, properly labeled image to your Wikispaces page and labnoteook
 * 4) Once you have chosen your target: Protocol Primer Design for Overlap PCR - post final primers to Wikispaces page
 * ProtocolPCR_PrimerDesign_for_pNIC-Bsa4Cloning.doc
 * 1) 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)

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
 * 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

Submit 2nd job of Virtual Screen Refresher Begin Virtual Screening on YOUR target Virtual Screening
 * 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 >
 * 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 **