The document provides a budget worksheet and project plan for sequencing the genome of a genetically modified E. coli sample. It includes costs for sequencing services, supplies, personnel, and a bioinformatics specialist to analyze the resulting data over a 6 month period. The total estimated cost for the project is $210,946.

1. BudgetProjections1YrProject.xlsx.xlsx
1YearProjectProposal Budget Worksheet, 1 Year ProjectFringe
Benefits Rate Non-Sponsored and Sponsored 07/01/2015-
06/30/2016This worksheet assumes that each subawardee will
be issued a new contract each year.Faculty and Classified
Staff36.30%Enter data in year 1 and it will be projected in all
future years using the indicated increment.Hourly8.50%Data
may be entered in any future year and it will be projected to the
end.Full-Time VCU Student0.00%Complements of Virginia
Commonwealth University**Facilities & Administration (F&A)
Rates (O/C = On campus; Off/C = Off Campus)07/01/13 – Until
notice:O/C Research52.50%Increment Rate 4.00%Non-
PersonnelOff/C Research26.00%Increment Rate
4.00%PersonnelO/C Instruction40.00%Fac. & Class.
Fringe36.30%Off/C Instruction26.00%Hourly Fringe
Rate8.50%O/C Other35.00%**F&A Rate (See
Chart)52.50%Off/C Other26.00%Restricted RatesOther Rates:
Legacy On Campus Res52.00%PersonnelOther Rates: Industry
Sponsored Clinical Trial25.00%Faculty & ClassifiedOther
Rates: Sponsor Restricted Other20.00%Name% EffortAnnual
SalaryYear 1Other Rates: Sponsor Restricted Local10.00%Dr.
Wu (Genentech)5%100,00016,250Other Rates: Sponsor
Restricted Training8.00%Project manager-Sr
Scientist25%60,00015,000Other Rates: Sponsor
Restricted5.00%Bioinformaticist25%60,00015,000Other Rates:
No F&A Allowed by Sponsor0.00%Sequencing Technician-
Sonya50%45,00022,5000%000%000%000%000%000%00Subtot
als68,750Summer & Part-Time FacultyName% EffortAnnual
SalaryYear
10%000%000%000%000%000%000%000%000%00Subtotals0H
ourly & PostdoctoralNameHrs. WorkedRate Per HourYear
1Bioinformactist-
George20501,000000000000000000000000000000Subtotals1,00

2. 0Nonfringe & StudentsName% EffortAnnual SalaryYear
10%000%000%000%000%000%000%000%000%000%00Subtota
ls0Subtotal Personnel69,750Fringe Faculty &
Classified24,956Fringe Summer & Part-Time Faculty0Fringe
Hourly85Postdoctoral Health Ins.0Subtotal Fringe25,041Total
Personnel94,791Consultants(Names)000Subtotals0Equipment
(>$5,000
each)Servers0000Subtotals0Supplies(Itemize)MasterPure
Complete RNA & DNA Purification Kit376LB
media480000000Subtotals424Patient
CareInpatient0Outpatient0Subtotals
0Alterations/Renovations(Itemize)000Subtotals0Travel/Shippin
g(Itemize)Shipping E.coli from KY Genentech/Roche
location11000Subtotals110Other(Itemize)0VCU Complete Run
Supplies+Service10,000VCU Full Gene Expression Analysis
Supplies +Service25,000VCU Mate Paired Run Supplies +
Service8,0000Total RentRent00Total
TuitionTuition00Subtotals43,000Subtotal Direct Cost at
VCU138,325138,325SubawardsSubawardee
#1Direct0Indirect00Subawardee
#2Direct0Indirect00Subawardee
#3Direct0Indirect00Subawardee #4Direct0Indirect00Total
Direct Subawards0Total Indirect Subawards0Total
Direct138,325F&A Base138,325Total F&A72,621Total
Costs210,9461-year DC total138,3251-year F&A base138,3251-
year F&A total72,6211-yr total cost210,946For NIH
Applications:Total VCU Direct
Costs138,325Consortium/Contractual Direct Costs0Subtotal
Direct Costs for Initial Budget Period (Item 7a, Face
Page)138,325Consortium/Contractual F&A Costs0Total Direct
Costs for Initial Budget Period138,325
__MACOSX/._BudgetProjections1YrProject.xlsx.xlsx
Management Plan.pptx

3. High Throughput Sequencing of a Genetically Modified
Microbe
Project Management Plan
1
Project Definition
Develop a budget estimate and operating plan for the
sequencing of the genome of a genetically modified
microorganism, E.coli.
Image Credit: http://s.wsj.net/public/resources/images/OB-
ZC073_0930ec_F_20130930040254.jpg
2
Project Summary
Dr. Wu of Genentech
Genetically Modified E. coli
Characterize the complete genome
Characterize the complete transcriptome
Develop a project plan and a cost estimate
Image Credit: http://www.cbc.ca/news/technology/scientists-
design-gmos-that-can-t-escape-into-the-wild-1.2929554
3
Bioinformatic Analysis

4. Image Credit:
http://www.tgac.ac.uk/uploads/images/_DSC3572%20copy.jpg
http://www.jscimedcentral.com/Bioinformatics/images/Bioinfor
matics-banner4.jpg
Measure of Success: High quality analysis
Milestone of Progress: Complete processing of all data
Now it’s a time for some computational power
As a bioinformatics
Wet lab result
Analyze the data by Writing bunch of codes for
arranging the genome sequence, discover the mutation and
modify the gene, and find the differences in the genome.
4
Results Assessment & Presentation to Dr. Wu
Image Credit: http://www.chicagonow.com/healthy-
human/files/2015/12/97330-93928.jpg
http://dna.cs.byu.edu/bio465/puzzle.png
Measure of Success: Dr. Wu accepts the proposal
Milestone of Progress: Complete review and presentation
Deliverables
Whole Genome Sequence
Distance between Genes
RNA Expression Data
Understanding of the genetically modified microbe

5. Image Credit:
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastq
c.png
https://seqcore.brcf.med.umich.edu/sites/default/files/images/no
rmal3730.gif
Required Resources
VCU Sequencing Core Facilities
DNA extraction kits
Thermocycler
Pipettes
Nanodrop or Qbit analyzer
Library preparation kit
Sequencing reagents
Sample index kit
Freezer and fridge
Sequencer
Computer for data analysis
Image Credit:
http://hihg.med.miami.edu/images/sized/images/_MG_685623ne
wL-460x215.jpg
Required Resources
LB Broth
Erlenmeyer flasks
Test Tubes
Wu’s VCU collaborator’s lab
Bacterial Incubator
Bacterial Incubator/Shaker
Freezer
Fume Hood
Genetically Modified E.coli Sample

6. Image Credit:
http://hihg.med.miami.edu/images/sized/images/_MG_685623ne
wL-460x215.jpg
Good Laboratory Practices
21 CFR Part 58
Standard Sequencing Protocols
Standard DNA & RNA Extraction
Lab Notebooks
Adequate Facility
Lab Coats
Lab Gloves
Separate Rooms for Isolation
Storage of Sequence Data
Image Credit: http://www.esus.ie/projects-
elearning/1/GoodLaboratoryPractice.png
Timetable for TrackingTaskStart DateTime (days)E.coli
Shipment1-Jun2E.coli Growth3-Jun1DNA & RNA purification
Kit4-Jun1Sequencing4-Jun90Bioinformatic Analysis4-
Sep90Results Assessment/Presentation22-Sep14
CostPersonnelYear 1 CostDr. Wu (Genentech)16,250Project
Manger-Sr. Scientist15,000Bioinformaticist15,000Sequencing
Technician22,500Data Manager1,000Fringe
Benefits25,041F&A93,706SuppliesYear 1 CostMasterPure
Complete RNA & DNA Purification Kit376LB
media48Total424ShippingYear 1 CostShipping E.coli from KY
Genentech location110OtherYear 1 CostVCU Complete Run
Supplies+Service10,000VCU Full Gene Expression Analysis

7. Supplies +Service25,000VCU Mate Paired Run Supplies +
Service8,000Total43,000
Total Cost for Project: 210,946
Recap Milestones & Measures
Task 1:
Milestone of progress: Viable E.coli arrived in the VCU lab
Task 2:
Measure of Success: Genetically modified bacteria grow and
grow to a healthy concentration (108)
Milestone of Progress: E.coli grows
Task 3:
Measure of Success: The DNA and RNA are pure; the
concentration high
Milestone of Progress: Isolation of DNA and RNA
Task 4:
Measure of Success: Get good quality results
Milestone of Progress: Complete the sequencing of the whole
genome
Recap Milestones & Measures
Task 5:
Measure of Success: Get good quality results
Milestone of Progress: Complete the sequencing of the mate
paired analysis
Task 6:
Measure of Success: Get good quality results
Milestone of Progress: Complete the expression analysis
Task 7:
Measure of Success: High quality analysis
Milestone of Progress: Complete processing of all data
Task 8
Measure of Success: Dr. Wu accepts the proposal
Milestone of Progress: Complete review and presentation

8. Executive Summary
Mission: Develop a project management plan to characterize a
genetically modified E.coli
Objectives:
Obtain Whole Genome Sequence
Expression Analysis of Genome
Distances between Genes
Cost for a year is $209,291
Project Duration: 6 Months
References
__MACOSX/._Management Plan.pptx
Project II High throughput sequencing modified microbe.docx
Project II High throughput sequencing of a genetically
modified microbe
The Solexa high though-put sequencer is the one of the fastest
gene sequence analyzers in the world. Having successfully
inserted some genes into e. coli to create a new mutant
microorganism, molecular geneticist Dr. Wu of Genentech
wants to characterize the complete genome of the mutant. You
have been asked by Dr. Wu to give him a cost estimate for this
work. If the following laboratory analyses and bioinformatics
data analysis are required, determine the cost for this project for
Dr. Wu.

9. One complete run on the high throughput Solexa sequencing
instrument is needed at a cost of $10,000 in service charges
from the VCU Genome Sequencing Center. In addition one full
gene expression analysis on the Solexa at a cost of $2500 is
required, as well as two additional mate paired runs on the
Solexa at a cost of $4000 each. The sequencing will take about
two weeks effort by a post doctoral scientists paid $45,000
annually. The labor for the laboratory sequencing work is
included in the service center cost, but the cost for the
bioinformatics data analysis is not. The High Performance
Computing Center at VCU houses adequate computing
capability, but the cost for the time and effort of a masters
degree bioinformatics specialist must be covered by the project.
The data analysis will require determination of genome
arrangement, mutation discovery and differentiation. The time
estimated for the bioinformatics specialist may vary somewhat,
but we estimate that it will take three months. The overhead is
covered by the university Facilities and Administration cost,
which is 50% on research projects such as this. If the BNFO
specialist is paid $60,000 annually and his/her fringe benefits
rate is 33.3%, develop a budget for Dr. Wu and justify each
item for this laboratory research project.
__MACOSX/._Project II High throughput sequencing modified
microbe.docx
Project II Project Management Plan Report Guide.docx
Project II Project Management Plan Report Guide
5. Objectives and deliverables
6. Tasks and timeline

10. 7. Budget work sheet (as an Excel spreadsheet) with spaces for
personnel, supplies, materials, equipment, travel, and other
(including contracts for major equipment installation or
maintenance contracts for equipment). This is the spreadsheet
the university likes to use for research proposals. This is for
your project management budget
8. Budget narrative
10. References
__MACOSX/._Project II Project Management Plan Report
Guide.docx
Unit 3.2 from the supplement book: Should Abortion be
Restricted?
Minimum 5 full and complete pages: Name, section, etc go on a
cover page
of policy, politics and controversy
ok, what are the main arguments
from each side? Remember, this is
the main part of your paper. Read the unit thoroughly and
discuss the “for” side and “against”
side.

11. the issue and explore what has been
going on at the national and state levels in the last couple of
years: What have some states been
doing in terms of state legislation to further restrict abortion?
What national Supreme Court
ruling is in effect today? These are just a couple of questions;
explore more on your own.
you think? What is your opinion?