Timeline+F15

=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.

Looking for the **Presentation Schedule**? - see the Schedule Fall15 ( 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 **=== ||
 * SPRINGERS **WEEK 15**

Finish up research for the semester. All ligands should be docked Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library.

Final 5 compounds can be uploaded to Screened Compounds spreadsheet on GDocs @https://docs.google.com/spreadsheets/d/1pFn32b7cq9xZP8GIjWB1cTieH4xvGFmCJnUNdXt1ecs/edit?usp=sharing
 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf

If you got to secondary PCR, you should have tried a cloning round.

Computer Lab Help session 3-5
 * 30-Nov Monday**

Peer Review of M&M Expr, Pur, Char
 * 1-Dec Tuesday**

Class A - 2-3 PM
 * 2-Dec Wednesday**

Computer Lab Help session 3-5

Class B - 5-6 PM Lab cleanup -see sheet for items. Then have a mentor sign you off on the line for the things you completed @https://drive.google.com/file/d/0B_Gl3lMyhDsoc21pYmJlc3lSbXM/view?usp=sharing
 * 3-Dec Thursday**

Just Added! Computer Lab Help session 2-6 (in the Other computer lab WEL 2.144)

Computer Lab Help session 3-6
 * 4-Dec Friday**

Lab cleanup -con't

Final Report due at 9pm Wikispaces due
 * 5-Dec Saturday**
 * 6-Dec Sunday**

Final Notebook due at 9pm || VETERANS **WEEK 15**
 * 7-Dec Monday**

Finish up research for the semester. All ligands should be docked If you got to secondary PCR, you should have tried a cloning round.

Final 5 compounds can be uploaded to Screened Compounds spreadsheet on GDocs @https://docs.google.com/spreadsheets/d/1pFn32b7cq9xZP8GIjWB1cTieH4xvGFmCJnUNdXt1ecs/edit?usp=sharing

Peer Review of M&M Expr, Pur, Char
 * 30-Nov Monday**
 * 1-Dec Tuesday**

Class A - 2-3 PM
 * 2-Dec Wednesday**

Class B - 5-6 PM Lab cleanup -see sheet for items. Then have a mentor sign you off on the line for the things you completed @https://drive.google.com/file/d/0B_Gl3lMyhDsoc21pYmJlc3lSbXM/view?usp=sharing
 * 3-Dec Thursday**

Lab cleanup - con't
 * 4-Dec Friday**

Final Report due at 9pm Wikispaces due
 * 5-Dec Saturday**
 * 6-Dec Sunday**

Final Notebook due at 9pm ||
 * 7-Dec Monday**
 * ===** Next Week **=== || ===** Next Week **=== ||
 * ===** Next Week **=== || ===** Next Week **=== ||
 * ===** Next Week **=== || ===** Next Week **=== ||

Create/Update Target page on Wikispaces for your Team's target



LabNotebooks A, B, C, D, .... Wikispaces (Bi-Weekly) Safety Target Page LICpNIC-Bsa4cloningExercise Misc mini-assignments or quizzes 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
 * List of Assignments:**

**2 Weeks Blocks layout**
26-Aug Wednesday - 6-Sep Sunday (1.5 wks) 7-Sep Monday - 20-SepSunday 21-SepMonday - 4-Oct Sunday 5-Oct Monday - 18-OctSunday 19-OctMonday - 1-Nov Sunday 2-Nov Monday - 15-Nov Sunday 16-Nov Monday - 29-Nov Sunday 30-Nov Monday - 6-Dec Sunday
 * In general your progress will be assessed every 2 weeks (lab hours, research progress, wikispaces updates)**

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 captions to let the reader (Dr. B) understand what it is.
 * **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) || mmmmm ||
 * 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) - 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_Fall15.doc - 2 hrs
 * upload final primers to Google Docs/VDS/Misc/Primers/**PrimerPlateOrderFall2015**
 * 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 for your own primers

Create or Revise your Target page (not same as your Research Page) LICpNIC-Bsa4cloningExerciseVDS_Fall15

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**

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 ......
 * Graded Assignments:**
 * HOURS:**

2015 Dates:

Yes - you do need lab hours for week 1 (just 4 hrs - so, get in lab and review your notebook & plan)
 * **Week1**

sign up for Fire Safety training (see link to left 'Required Lab Safety') Lab times open for Nanodrop and Submit to DNA sequencing
 * 26-Aug Wednesday**
 * 27-Aug Thursday**

See Submit to DNA Sequencing protocol (in GDrive/Protocols) for Instructions: 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**

Print protocols as '2 sheets per page' Nanodrop protocol Submit to DNA Sequencing

Create your Research Page on Wikispaces and post your first results - see page for Instructions

Yes - you do need lab hours for week 1 (just 3-4 hrs - so, get in lab and review your notebook & plan)
 * 28-Aug Friday**
 * 29-Aug Saturday**
 * 30-Aug Sunday** || **Week1**

planning startup your cloning work again
 * 26-Aug Wednesday**
 * 27-Aug Thursday**

planning startup your cloning work again
 * 28-Aug Friday**


 * 29-Aug Saturday**
 * 30-Aug Sunday** ||
 * **WEEK 2**

Be sure you have 8-10hrs/week
 * - for the 1st week of class that should be about 2-3 hrs since the lab was only open for 2 days**

See Week1 items at bottom of page for things that you didn't get to.

Items for 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 **
 * create your ** Research Page ** on Wikispaces
 * Transform pNIC-Bsa4 into DH5alpha (with a partner) - use 'homemade' competent cells (NOT THE NEB ones) - sign up for specific times
 * -- ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v5.doc
 * Make 500ml of LB and autoclave (with mentor) - anytime mentor available
 * Dilute some primers (if they come in) - anytime mentor available
 * RE Digest - at specific times
 * Dilute some primers (if they come in) - anytime mentor available
 * RE Digest - at specific times
 * RE Digest - at specific times

For protocols, look in GDrive/VDSClass/Protocols/FirstProtocols

Transformation times (must start on time) Make 500ml of LB and autoclave (with mentor)
 * 31-Aug Monday**

Transformation times (must start on time) Make 500ml of LB and autoclave (with mentor)
 * 1-Sep Tuesday**

Class A - 2-3 PM Location: see the Schedule Fall 15 (Semesterly) Class B - 5-6 PM Location: GEA 125
 * 2-Sep Wednesday**

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)


 * 3-Sep Thursday**

RE Digest


 * 4-Sep Friday**

RE Digest

Lab Notebook @ 5pm - lab will be open for notebooks - no mentors on staff yet. So, if you need the lockbox code - email Andee or one of the mentors. Springers should not be doing lab work on Saturdays. Only Veterans can do Saturday work right now.
 * 5-Sep Saturday**

Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015 || **WEEK 2**
 * 6-Sep Sunday**

Get some hours in lab PyMol refresher exercise - see/GDrive/Protocols/VirtualProtocols

Class A - 2-3 PM Location: see the Schedule Fall 15 (Semesterly) Class B - 5-6 PM Location: GEA 125
 * 31-Aug Monday**
 * 1-Sep Tuesday**
 * 2-Sep Wednesday**
 * 3-Sep Thursday**
 * 4-Sep Friday**

- no mentors on staff yet. So, if you need the lockbox code - email Andee or one of the mentors. Springers should not be doing lab work on Saturdays. Only Veterans can do Saturday work right now and must be with another equally trained VDSer.
 * 5-Sep Saturday**

Wikispaces posting due - 9 pm || Items for This Week
 * 6-Sep Sunday**
 * **WEEK 3**
 * RE Digest gel check
 * Analyze DNA Sequence -in comp lab
 * Grow up 160 ml of pNIC-Bsa5 and save for later.


 * 7-Sep Monday - Labor Day - No Lab**

4-6:30 pm - Analyze DNA Sequence Exercise (as a group) - in WEL 2.144 Comp Lab
 * 8-Sep Tuesday**

Class A - 2-3 PM Location: PAI 5.33 Class B - 5-6 PM Location: GEA 125
 * 9-Sep Wednesday**

Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):
4, 5 or 6 PM (takes 1 hour) - 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. In order to make lots of plasmid that we will need for cloning: -- Plasmid Midi-prep (in pairs) - use Tony's new protocol

come in to lab in morning to spin down overnight cultures 3:30 -6:30 pm - Analyze DNA Sequence Exercise (as a group) - in WEL 2.144 Comp Lab
 * 10-SepThursday**

Grow up DH5alpha cells for Plasmid Preps (just store pellets though - don't do MidiPrep yet):
4, 5 or 6 PM (takes 1 hour)

ProtocolPCRVDS.xls -

come in to lab in morning to spin down overnight cultures Analyze RE digest on a gel ProtocolPCRVDS.xls
 * 11-SepFriday**


 * 12-SepSaturday**
 * 13-SepSunday** || **WEEK 3**


 * Virtual Work**


 * PyMol Refresher:** Virtual Volunteers from summer don’t have to do this! (Kevin H, Bethany, Jeff, Lisa, Steven, Diane)
 * can count as 2 hours of lab time

start Virtual Screening Refresher - see GDocs/Protocols/VirtualProtocols


 * 7-Sep Monday - Labor Day - No Lab**

4-6:30 pm - PyMol & Virtual Screening help in WEL 2.144 Comp Lab
 * 8-Sep Tuesday**

Class A - 2-3 PM Location: PAI 5.33
 * 9-Sep Wednesday**

Class B - 5-6 PM Location: GEA 125


 * 10-SepThursday**

4-6:30 pm - Virtual Screening help in WEL 2.144 Comp Lab

PyMol Refresher - due


 * 11-SepFriday**

Create/Update Target page on Wikispaces for your Team's target


 * 12-SepSaturday**
 * 13-SepSunday** ||
 * **WEEK 4**

Items for This Week Maybe:
 * 'My First PCR' - using pGBR22 (repeat until it works)
 * - ProtocolPCRVDS.xls
 * Run gel to check it
 * Target Selection Form - once Dr. B sends the link
 * PyMol Refresher
 * MidiPrep of your pNIC-Bsa4 that you grew up last week
 * Second Practice PCR (pLIC primers on pNIC-Bsa4): ProtocolPCR_pLICsequencing15.xl
 * Oligo Primer Design
 * Tail Primer Design and Ordering

1st Mini Meetings - All Groups
 * 14-SepMonday**
 * 15-SepTuesday**

Class A - 2-3 PM Location: PAI 5.33
 * 16-SepWednesday**

Class B - 5-6 PM Location: GEA 125


 * 17-SepThursday**
 * 18-SepFriday**


 * 19-SepSaturday**

Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015 || **WEEK 4**
 * 20-SepSunday**

Create/Update Target pages


 * 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

Virtual Refresher Help Session ?
 * 14-SepMonday**
 * 15-SepTuesday**

1st Mini Meetings - All Groups

Class A - 2-3 PM Location: PAI 5.33
 * 16-SepWednesday**

Virtual Refresher Help Session?

Class B - 5-6 PM Location: GEA 125

Virtual Refresher Help Session Virtual Screening Refresher due
 * 17-SepThursday**


 * 18-SepFriday**

Wikispaces Research Pages posting due - 9 pm http://vdsstream.wikispaces.com/Research+Pages+2015 || Items for This Week
 * 19-SepSaturday**
 * 20-SepSunday**
 * **WEEK 5**
 * Repeat - 'My First PCR' - if failed
 * Second Practice PCR (pLIC primers on pNIC-Bsa4): ProtocolPCR_pLICsequencing15.xl
 * Oligo Primer Design
 * Tail Primer Design and Ordering
 * PyMol Refresher
 * Make Oligo Mix for your targets (each person makes own)
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx

Scheduled Times for Lab @https://docs.google.com/spreadsheets/d/1QK6fn8avAAYZ6SJb8GStMUCcPc1zKRMzpUrXuQhegqQ/edit?usp=sharing

Oligo Primer Design & Ordering for Targets
 * 21-SepMonday**

Oligo Primer Design & Ordering for Targets
 * 22-SepTuesday**

Class A - 2-3 PM Location: PAI 5.33
 * 23-SepWednesday**

Class B - 5-6 PM Location: GEA 125

6-7:30 PyMol Refresher Help session in WEL 2.128
 * 24-SepThursday**
 * can count as 2 hours of lab time

3-5:30 PyMol Refresher Help session in WEL 2.128
 * 25-SepFriday**
 * can count as 2 hours of lab time

PyMol Refresher - due for springers
 * 26-SepSaturday**

Lab Notebook @ 5pm - lab will be open for notebooks PyMol Refresher Analyze DNA Sequence RE Digest PCR & run on an agarose gel (if done) Oligo Design - protocol and DNA Works output file Tail Primer Design - protocol and results of what you are ordering
 * What Goes Where for notebook?:**


 * 27-SepSunday**

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15 || **WEEK 5** Class A - 2-3 PM Location: PAI 5.33
 * 21-SepMonday**
 * 22-SepTuesday**
 * 23-SepWednesday**

Class B - 5-6 PM Location: GEA 125


 * 24-SepThursday**
 * 25-SepFriday**

Lab Notebook @ 5pm - lab will be open for notebooks
 * 26-SepSaturday**


 * 27-SepSunday**

Not due yet, but Mid Semester Research Report Guidelines posted to: GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15 .doc || Items for This Week
 * **WEEK 6**
 * Second Practice PCR (pLIC primers on pNIC-Bsa4): - on your own - ProtocolPCR_pLICsequencing15.xl
 * Make Oligo Mix for your targets
 * each person makes own
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx
 * Primary PCR
 * ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall14.docx

Schedule for this week:

Mini Meetings for ALL this time
 * 28-SepMonday**
 * 29-SepTuesday**

2pm - Bacteria 2:30 pm - Fungi 5pm - Protozoa 5:30 pm - Viruses

Class A - 2-3 PM
 * 30-SepWednesday**

Class B - 5-6 PM

Virtual Screening Refresher - start looking at will be due next week
 * 1-Oct Thursday**
 * 2-Oct Friday**


 * 3-Oct Saturday**

Mid Semester Research Report Due GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15 || **WEEK 6**
 * 4-Oct Sunday**

Items for This Week
 * Control ligands should be selected (Pos & Neg)
 * LigPrep your control ligands
 * Select your protein structure, run Molprobity on it, Upload to DDFE
 * Determine active site and which substrates/metals should or should not be in place
 * Dock control ligands

VS Help Session times with Dr. B - Mon - Tues ? - Wed, - Thurs - Fri

Mini Meetings for ALL this time
 * 28-SepMonday**
 * 29-SepTuesday**

2pm - Bacteria 2:30 pm - Fungi 5pm - Protozoa 5:30 pm - Viruses

Class A - 2-3 PM
 * 30-SepWednesday**

3-5: VS Help Session - in 'main' Comp Lab (WEL 2.128)

Class B - 5-6 PM


 * 1-Oct Thursday**

VS Help Session - in 'other' Comp Lab (WEL 2.144)


 * 2-Oct Friday**


 * 3-Oct Saturday**

Mid Semester Research Report Due GDocs/__Results&Data__/ResearchReport/ GuidelinesResearchReportonTargetMidSemester_VDS_Fall15 ||
 * 4-Oct Sunday**
 * **WEEK 7**
 * Items for the Week**
 * Finish practice PCRs
 * you must have a working practice PCR (either pGBR22 or pNIC pcr. If you aren't sure - let Dr. B check it on your Research Page)
 * Virtual Screening Refresher (worth 2hrs of lab time)
 * Primary PCR
 * Primer Dilution of your own tail primers (you've done a primer dilution before)
 * Secondary PCR

Wet lab will be Open Times this week - just come in whenever a mentor is present. Shoot for 8-10 hrs at least for the week while moving your project forward.

2:30 - 6pm WEL __2.128__ Help Session - VS Refresher & Mid Semester Res Report 3-6 Mentors on staff in wet lab
 * 5-Oct Monday**

no mini-meetings 4 - 6:30 pm WEL **2.144** Help Session - VS Refresher & Mid Semester Res Report
 * 6-Oct Tuesday**

3-6 Mentors on staff in wet lab

Class A - 2-3 PM
 * 7-Oct Wednesday**

3-5pm WEL __2.128__ Help Session - VS Refresher & Mid Semester Res Report 3-6 Mentors on staff in wet lab

Class B - 5-6 PM

3:30 - 6:30 pm WEL **2.144** Help Session - VS Refresher & Mid Semester Res Report 3:30 -7 Mentors on staff in wet lab
 * 8-Oct Thursday**

2:30 - 4:30 pm WEL __2.128__ Help Session - VS Refresher 2-6:30 Mentors on staff in wet lab
 * 9-Oct Friday**


 * 10-OctSaturday**
 * 11-OctSunday** || **WEEK 7**
 * Items for the Week**
 * finish Control Ligs docking (discuss with Dr.B)
 * start docking of a medium library (e.g. CB306 and Maybridge HF9)
 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf


 * finish cloning .......

See the Springers side for the Virtual Help sessions

no mini meetings Class A - 2-3 PM
 * 5-Oct Monday**
 * 6-Oct Tuesday**
 * 7-Oct Wednesday**

Class B - 5-6 PM


 * 8-Oct Thursday**
 * 9-Oct Friday**
 * 10-OctSaturday**
 * 11-OctSunday** ||
 * **WEEK 8**
 * Items for the Week**
 * Tail Primer dilution
 * Secondary PCR
 * PCR squared
 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands

4:30- 6:30 pm WEL __2.128 (or maybe WEL 2.144)__ Help Session - VS Refresher Open Labs: 3:30-7
 * 12-OctMonday**

Mini Meetings for some Open Labs: 3:00 -7
 * 13-OctTuesday**

Class A - 2-3 PM
 * 14-OctWednesday**

Open Labs: 3:00-7

Class B - 5-6 PM

Open Labs: 3:00-7
 * 15-OctThursday**

Open Labs: 2-7
 * 16-OctFriday**

Lab Notebook due
 * 17-OctSaturday**

Target Page due for Springers (see Target pages on Wikispaces) Peer Review of Mid Semester Research Report due || **WEEK 8**
 * 18-OctSunday**
 * Items for the Week**
 * finish docking of a medium library
 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf
 * Start docking of
 * Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf
 * Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf


 * finish cloning .......

Mini Meetings for some Class A - 2-3 PM
 * 12-OctMonday**
 * 13-OctTuesday**
 * 14-OctWednesday**

Class B - 5-6 PM


 * 15-OctThursday**
 * 16-OctFriday**
 * 17-OctSaturday**
 * 18-OctSunday** ||
 * **WEEK 9**
 * Items for the Week**
 * Secondary PCR
 * PCR squared
 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands
 * Start cloning rounds
 * Pick control ligands for VS

Mini Meetings for some Class A - 2-3 PM
 * 19-OctMonday**
 * 20-OctTuesday**
 * 21-OctWednesday**

Class B - 5-6 PM

Lab Notebook due pNIC-Bsa4 exercise do (on paper) - put in your notebook as loose leaf
 * 22-OctThursday**
 * 23-OctFriday**
 * 24-OctSaturday**

M&M Cloning due - see Canvas for link || **WEEK 9**
 * 25-OctSunday**
 * Items for the Week**
 * continue docking of
 * Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf
 * start protein expression trial

Mini Meetings for some Class A - 2-3 PM
 * 19-OctMonday**
 * 20-OctTuesday**
 * 21-OctWednesday**

Class B - 5-6 PM

Lab Notebook due pNIC-Bsa4 exercise do (on paper) - put in your notebook as loose leaf
 * 22-OctThursday**
 * 23-OctFriday**
 * 24-OctSaturday**

M&M Cloning due - see Canvas for link ||
 * 25-OctSunday**
 * **WEEK 10**


 * Items for the Week**
 * PCR squared
 * Pick control ligands for VS (see computer lab times for help)
 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands
 * Start cloning rounds
 * Dock control ligands for VS

Control Ligands Instructions: (WITHIN the shared folder), and split the positive and negative ligands between each member. Split the positive ligands evenly amongst the group and then each person should do at least 2 negative control ligands.
 * Make folder for target in /Projects Folder in VDS Class.
 * Create a Google Spreadsheet for your control ligands
 * Then place copies of your downloaded ligands into the folder
 * When you start your Lig Prep for virtual screening – upload the ligands files into your own folder on the DDFE

Wet Lab: check the calendar for when mentors will be on to help

Comp lab help: 3-5 pm
 * 26-OctMonday**

Mini Meetings for some
 * 27-OctTuesday**

Class A - 2-3 PM Comp lab help: 3-5 pm Class B - 5-6 PM
 * 28-OctWednesday**


 * 29-OctThursday**

Comp lab help: 3-5 pm
 * 30-OctFriday**

Finish picking control ligands
 * 31-OctSaturday**

Peer Review of M&M Cloning Due Wikispaces due Weeks 8,9,10 || **WEEK 10**
 * 1-Nov Sunday**


 * Items for the Week**
 * finish docking of
 * Screen 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf
 * express protein
 * purify protein
 * enzyme assay test

Mini Meetings for some Class A - 2-3 PM
 * 26-OctMonday**
 * 27-OctTuesday**
 * 28-OctWednesday**

Class B - 5-6 PM

Peer Review of M&M Cloning Due Wikispaces due Weeks 8,9,10 ||
 * 29-OctThursday**
 * 30-OctFriday**
 * 31-OctSaturday**
 * 1-Nov Sunday**
 * **WEEK 11**


 * Items for the Week**
 * PCRs
 * Dock control ligands for VS (see computer lab times for help)
 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands
 * Start cloning rounds
 * Dock control ligands for VS

Wet Lab: check the calendar for when mentors will be on to help

Start to dock control ligs 3-5 pm computer lab help session WEL 2.128
 * 2-Nov Monday**

Mini Meetings for some Class A - 2-3 PM 3-5 pm computer lab help session WEL 2.128 Class B - 5-6 PM
 * 3-Nov Tuesday**
 * 4-Nov Wednesday**

3-5 pm computer lab help session WEL 2.128
 * 5-Nov Thursday**
 * 6-Nov Friday**

Finish docking control ligs
 * 7-Nov Saturday**

M&M Virtual due || **WEEK 11**
 * 8-Nov Sunday**


 * Items for the Week**
 * analyze results of
 * Screening 25,000 ligands of CBZincpH7/cbbr_p0.7.sdf
 * finish cloning
 * express protein
 * purify protein
 * enzyme assay test

Mini Meetings for some Class A - 2-3 PM
 * 2-Nov Monday**
 * 3-Nov Tuesday**
 * 4-Nov Wednesday**

Class B - 5-6 PM

M&M Virtual due ||
 * 5-Nov Thursday**
 * 6-Nov Friday**
 * 7-Nov Saturday**
 * 8-Nov Sunday**
 * **WEEK 12**
 * 9-Nov Monday**


 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands
 * Start cloning rounds

start docking of medium libraries
 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf

Mini Meetings for some Class A - 2-3 PM
 * 10-Nov Tuesday**
 * 11-Nov Wednesday**

3- 5- Computer Lab help session WEL 2.128

Class B - 5-6 PM


 * 12-Nov Thursday**
 * 13-Nov Friday**

3- 5- Computer Lab help session WEL 2.128

Lab Notebook Due
 * 14-Nov Saturday**


 * 15-Nov Sunday**

24th -NOV finish docking of a medium libraries
 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf || **WEEK 12**


 * Items for the Week**
 * upload top 5 compunds to ScreenedCompounds spreadsheet in GDrive
 * finish cloning
 * express protein
 * purify protein
 * enzyme assay test...

Mini Meetings for some
 * 9-Nov Monday**
 * 10-Nov Tuesday**

Class A - 2-3 PM
 * 11-Nov Wednesday**

Class B - 5-6 PM

Lab Notebook Due
 * 12-Nov Thursday**
 * 13-Nov Friday**
 * 14-Nov Saturday**


 * 15-Nov Sunday** ||
 * **WEEK 13**
 * Cut your pNIC-Bsa4 with BsaI restriction enzyme (see cloning protocol)
 * gel check it to confirm 2 bands
 * Start cloning rounds

Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library.


 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf

Wet Lab: check the calendar for when mentors will be on to help

4 - 5:30- Computer Lab help session WEL 2.128
 * 16-Nov Monday**

Mini Meetings for some Class A - 2-3 PM
 * 17-Nov Tuesday**
 * 18-Nov Wednesday**

3- 5- Computer Lab help session WEL 2.128

Class B - 5-6 PM


 * 19-Nov Thursday**

Just Added ! 2-6- Computer Lab help session WEL 2.144 (the other comp lab)

3- 5- Computer Lab help session WEL 2.128
 * 20-Nov Friday**


 * 21-Nov Saturday**
 * 22-Nov Sunday** || **WEEK 13**


 * Items for the Week**
 * upload top 5 compounds to ScreenedCompounds spreadsheet in GDrive
 * finish cloning
 * express protein
 * purify protein
 * enzyme assay test...


 * 16-Nov Monday**

Mini Meetings for some
 * 17-Nov Tuesday**

Class A - 2-3 PM
 * 18-Nov Wednesday**

Class B - 5-6 PM

continue cloning - if your Secondary PCR works - you should attempts a cloning roung.
 * 19-Nov Thursday**
 * 20-Nov Friday**
 * 21-Nov Saturday**
 * 22-Nov Sunday** ||
 * **WEEK 14**

Virtual Compile results of dockings into table with scores and physico chemical properties of Top 5 from each small library.


 * HF9PlatesPlates5_9.sdf
 * cb_306_3d.sdf
 * LOPAC_3d.sdf
 * NIH_ClinCol3Ded.sdf

Computer Lab Help session 3-6 Wet lab open
 * 23-Nov Monday**

Wet lab open
 * 24-Nov Tuesday**

No Class wet lab open
 * 25-Nov Wednesday**


 * 26-Nov Thursday - THANKSGIVING**
 * 27-Nov Friday**
 * 28-Nov Saturday**
 * 29-Nov Sunday** || **WEEK 14**

finish virtual finish cloning test your enzyme

No Class
 * 23-Nov Monday**
 * 24-Nov Tuesday**
 * 25-Nov Wednesday**
 * 26-Nov Thursday - THANKSGIVING**
 * 27-Nov Friday**
 * 28-Nov Saturday**
 * 29-Nov Sunday** ||