EPA/600/B-15/316
Quantitative Microbial Risk Assessment Tutorial
SDMProjectBuilder: Import Local Data Files to Identify and
Modify Contamination Sources and Input Parameters
Gene Whelan
Rajbir Parmar
Kurt Wolfe
Michael Galvin
U.S. Environmental Protection Agency
Office of Research and Development
National Exposure Research Laboratory
Ecosystems Research Division
Athens, GA 30605
Paul Duda
Mark Gray
AQUA TERRA Consultants, a Division of RESPEC, INC.
Decatur, GA 30030
11/20/15

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Summary
Twelve example local data support files are automatically downloaded when the SDMProjectBuilder is
installed on a computer. They allow the user to modify values to parameters that impact the release,
migration, fate, and transport of microbes within a watershed, and control delineation of a watershed
into subwatersheds. They represent templates for site-specific information, so data included in these
files, when initially downloaded, provide only an example format for the data which must be modified to
reflect conditions associated with the site being assessed. To specifically represent the user's watershed,
separate files must be created using the formatted templates to replace existing files; the files are in a
comma-separated variable (csv) format and, when modified, should be saved in a csv format. The files
providing location information as Latitude-Longitude pairs can also be individually edited within the
SDMProjectBuilder. Here, we review formats associated with the templates and explain information
contained in each file.
1

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SDMProjectBuilder:
Impc it f Ik > a\ I Kti i Files to Idt . . >ud Modify
Contamination Sources and IIinp	icteirs
PURPOSE
Consolidate information for gaining access to software used in support of Quantitative Microbial Risk
Assessment (QMRA) modeling.
OBJECTIVE
Describe 12 default local data files and their parameters which accompany the SDMProjectBuilder;
provide guidance on modifying values of these parameters which impact the release, migration, fate and
transport of microbes within a watershed; and describe steps to control delineation of a watershed into
subwatersheds.
GUIDANCE
This tutorial provides instructions and information on
•	Identifying locations of point and non-point sources of contamination;
•	Providing guidance for modifying values of parameters that impact the release, migration, fate
and transport of microbes within a watershed; and
•	Controlling delineation of a watershed into subwatersheds by identifying key locations that
represent subwatershed boundaries.
SOFTWARE ACCESS, RETRIEVAL, AND DOWNLOAD
The material in this document refers to the SDMProjectBuilder but does not require the user to access,
retrieve, and download the software. If interested, Whelan et al. (2015a) provides instructions for
access, retrieval, and download of the SDMProjectBuilder, HSPF, and BASINS software products.
2

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TECHNICAL CONTENT
DESCRIPTION OF THE 12 DEFAULT LOCAL DATA FILES
•	Domestic Animals, Wildlife, and Urban Built-up Area Loading Rates, and Microbial Die-off
o Domestic Animals
o Wildlife
o Urban Built-up Areas
o Microbial Die-off
•	Point Sources
•	Septic Systems
•	Intermediate Watershed Locations
o Output Locations
o Boundary Conditions
NAVIGATING THE SDMProjectBuilder TO IDENTIFY A HUC-8
IMPORTING LOCAL DATA FILES AS MAP LAYERS
SPECIAL NOTES ON IMPORTING POINT SOURCE TIME SERIES DATA
3

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DESCRIPTION OF THE 12 DEFAULT LOCAL DATA FILES
Twelve default local data files allow users to modify values of parameters that impact the release,
migration, fate, arid transport of microbes within a watershed, and control delineation of a watershed
into subwatersheds. Although a user-friendly interface to manage them does not currently exist, these
files allow users to modify input parameters that have a direct impact on determining microbial loadings
to a watershed. The files are included in the SDMProjectBuilder software download and stored in a
subfolder, "LocalData." The "LocalData" subfolder is concurrently created within the working folder,
when the working folder is created during execution of the SDMProjectBuilder. "TESTA" is an example
working folder illustrated in Figure 1, and the subfolder "LocalData" was automatically created to house
the 12 files.
Figure 1. Example of the 12 support files located in the "LocalData" subfolder within the "TESTA"
working folder

A.
~ Computer ~ OSDisk (G) ~ Users ~ gwhelan ~ iemTechnologies ~ SDMPB ~ TESTA ~ LocalData
File Edit View Tools Help
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[> NHDPIus
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Name
Q't PointSourceLL.csv
E3 OutputPointsLL.csv
WildlifeDensities.csv
ijT FCProdRates.csv
£3 SepticsDataWatershed.csv
(£|j SepticsLL.csv
fll] BoundaryPointsLL.CSV
0-. GrazingDays.csv
flaT| Mo nthlyFirstOrderDi eOffRateConstants.csv
§5] PointSourceData.csv
dll ManureApplication.csv
Q AnimalLL.csv
A list of the files with input data types, definitions, and units is presented in Table 1. A number of the
parameters are functions of domestic animal, wildlife, land use type, and/or urbanized built-up areas,
and are defined as follows:
Domestic animals in these files include dairy cow (DairyCow), beef cattle (BeefCow), swine
(Hog), sheep, horse, poultry (Chicken), turkey, dog, and other domestic agricultural animals
(OtherAgAnimal).
Wildlife include duck, goose, deer, beaver, raccoon, and other wildlife (OtherWildlife).
Four land use types are considered for any watershed: cropland, pasture, forest, and urbanized
built-up areas.
4

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Table 1. Names of the 12 default local data files and input types for which the user has access for
modifications
FILE NAME
INPUT DATA AND DEFINITION
UNITS
Domestic Animals and Wildlife
AnimalLLcsv
Domestic animal locations by Latitude and
Longitude
Degree (by
fraction)
Domestic animal numbers by type and
location
Number
FCProdRates.csv
Production or shedding rate of microbes
from the domestic animal, which equals the
multiple of the 1) Domestic animal shedding
rate in mass of waste (wet weight) per time
and 2) Microbial concentration based on
mass of waste shed by the domestic animal
Counts/d/animal
Typical microbial production or shedding
rate per wildlife per area
Counts/d/ac
GrazingDays.csv
Number of grazing days per domestic animal
per month
Number
Fraction of the number of grazing days that
Beef Cattle spend in a stream per month
fraction
ManureApplication.csv
Fraction of manure applied to soil each
month per domestic animal
fraction
Fraction of amount of manure shed by the
domestic animal incorporated into soil
fraction
MonthlyFirstOrderDieOffRateConstants.csv
First-order microbial inactivation/die-off
rate on the land surface per month
1/d
WildlifeDensities.csv
Typical number of wildlife per unit area by
land use type
Number/mi2
Point Sources
PointSourceLL.csv
Point source locations by Latitude and
Longitude
Degree (by
fraction)
PointSourceData.csv
Annual-average flow for each point source
ft3/s
Annual-average microbial loading rate for
each point source
Counts/yr
Annual-average chemical loading rate for
each point source
Lbs/yr
Septic Systems
SepticsLL.csv
Septic system locations by Latitude and
Longitude
Degree (by
fraction)
SepticsDataWatershed.csv
Number of people per septic unit
Number
Average fraction of septic systems that fail
fraction
Average septic overcharge rate per person
gal/d/person
Typical microbial density of septic
overcharge reaching the stream
Counts/L
Intermediate Points
BoundaryPoints.csv
Boundary point locations by Latitude and
Longitude
Degree (by
fraction)
OutputPoints.csv
Output point locations by Latitude and
Longitude
Degree (by
fraction)
5

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• Urbanized built-up areas include roads (Road), commercial property (Commercial), single-family-
low-density residence (SingleFamilyLowDensity), single-family-high-density residence
(SingleFamilyHighDensity), and multi-family residential (MultifamilyResidential). Single-family-
low-density is a single-detached dwelling, single-family residence, or separate house which is a
free-standing residential building (Wikipedia, 2015a). Single-family-high-density is a suite of
smaller scale single-family dwellings, representing a more compact single family residential
development (e.g., 13 -40 units/ac) (Garnett, 2012). Multi-family residential is a unit with
multiple separate housing units for residential inhabitants contained within one building, or
several buildings within one complex such as an apartment or condominium) (Wikipedia,
2015b).
These files only represent templates for capturing site-specific information, so their contents must be
updated to represent the user's specific site. Five of the 12 files provide location information, as
Latitude-Longitude pairs, and of these five, three allow the user to identify and manage sources of
microbial loadings:
1.	land-applied manure (AnimalLL.csv);
2.	point sources (PointSourceLL.csv) such as WWTP, POTW, etc.; and
3.	septic systems (SepticsLL.csv).
The other two location-based files (BoundaryPoints.csv and OutputPoints.csv) identify locations where
the user may want the watershed subdivided, such as sampling/monitoring locations. The remaining
seven files describe parameters that impact the actual loadings within a watershed. Whelan et al.
(2015b) describe how these parameters are used in the Microbial Source Module, which determines
microbial source loadings within a watershed. Use of these files are exemplified by Whelan et al. (2015c
2015d, 2015e, 2015f). Descriptions of each file are presented in the following sections.
Domestic Animals, Wildlife, and Urban Built-up Area Loading Rates, and Microbial Die-off
Domestic Animals
If domestic animals are located on the watershed, their locations should be reported using the
AnimalLL.csv template which captures the location of each animal source and number of animals at that
location. Farms are typically associated with these locations. An example of the AnimalLL.csv template is
presented in Table 2. These data are usually collected at the state level. At least one Latitude-Longitude
pair must be identified. If no sites are within the watershed, define one location and enter zeros for the
Latitude and Longitude. Locations of dairy farms in the Manitowoc River basin near Manitowoc, Wl are
shown in Figure 2. These were captured with Latitude-Longitude pairs, along with the number of
animals at each location, within the AnimalLL.csv template. If domestic animal sources are identified
through the AnimalLL.csv template (Table 2), the user must update the AnimalLL.csv (Table 2),
FCProdRates.csv (Table 3), GrazingDays.csv (Table 4), and ManureApplication.csv (Table 5) templates.
Microbial production rates, domestic animal grazing days, and fraction of the manure applied to the
land surface are documented in the FCProdRates.csv, GrazingDays.csv, and ManureApplication.csv
templates, respectively. If no animals are present, it is not necessary to modify FCProdRates.csv (Table
3), GrazingDays.csv (Table 4), and ManureApplication.csv (Table 5) templates, since no animals produce
microbial loadings. The user should not change column headings in any tables or row labels in Tables 3
through 5.
6

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Table 2. AnimalLL.csv template and example data
Latitude
Longitude
BeefCow
Swine
DairyCow
Chicken
Horse
Sheep
OtherAg
44.22582
-88.0305
0
0
0
0
0
0
0
44.2114
-88.0873
0
0
0
0
0
0
0
44.09547
-88.0263
0
0
0
0
0
0
0
44.23976
-88.0939
0
0
0
0
0
0
0
44.19051
-88.1283
0
0
0
0
0
0
0
44.22693
-88.1872
0
0
0
0
0
0
0
44.19139
-88.1327
0
0
0
0
0
0
0
44.18323
-88.146
0
0
0
0
0
0
0
44.22671
-88.1462
0
0
0
0
0
0
0
44.12401
-88.0751
0
0
0
0
0
0
0
44.2271
-88.2093
0
0
0
0
0
0
0
44.19682
-88.0229
0
0
0
0
0
0
0
44.1845
-88.1445
0
0
0
0
0
0
0
44.21851
-88.0042
0
0
0
0
0
0
0
44.12406
-88.0718
0
0
0
0
0
0
0
44.23874
-88.1834
0
0
0
0
0
0
0
44.17717
-88.0314
0
0
0
0
0
0
0
44.21836
-88.1342
0
0
0
0
0
0
0
44.20785
-88.0638
0
0
0
0
0
0
0
44.22697
-88.1897
0
0
0
0
0
0
0
44.21111
-88.0748
0
0
0
0
0
0
0
44.20104
-88.0435
0
0
0
0
0
0
0
44.19683
-88.0259
0
0
0
0
0
0
0
44.09548
-88.0354
0
0
0
0
0
0
0
44.23752
-88.0046
0
0
60
0
0
0
0
44.19700
-88.0954
0
0
0
0
0
0
0
44.16789
-88.0410
0
0
150
0
0
0
0
• •
• •
• •
44.05756
-88.1512
0
0
0
0
0
0
0
44.08862
-88.1774
0
0
0
0
0
0
0
43.97918
-87.8456
0
0
0
0
0
0
0
44.30336
-88.1727
0
0
0
0
0
0
0
43.91199
-88.3076
0
0
0
0
0
0
0
44.11344
-87.8003
0
0
0
0
0
0
0
44.12612
-88.2568
0
0
0
0
0
0
0
7

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Figure 2. Locations of dairy farms and assumed septic systems in the Manitowoc River basin near
Manitowoc, Wl. [Gray area designates the extent of the Manitowoc River basin, and farm and septic
locations are designated bv red dots,]
SDM Project Builder
File SDMProjectBuilder Extensions
iOQjfflS*	% % ~likH-Sl^ + 1
Legend | Selection [	
B ^ Map Layers
B ID BoundaryPointsLL
¦	
B 1^1 [Animals (Animais)|
B G SepticsLL
B O OutputPoinisLL
B O Point Sources (Point Sources)
¦
bD (NLDAS GridPoints) Role:MetStation
B El (NLDAS.GridSquares) Role:OtherBoundary
0 0 BASINS Met Station (MetStatlon) (met.shp) RoteMetStation
B ® NHDPIus Flowline (nhdflowline) (nhdflowline.shp) Role:Hydrography
B El NHDPIus Waterbody (nhdwaterbody) (nhdwaterbody.shp) Role:Hydrography
B 0 NHDPIus Catchment Polygons (catchment) (catchment.shp) RoleSubBasin
~
B C NHDPIus Flowline (nhdflowline) (nhdflowline.shp) Role:Hydrography
0 Q NLCD_20l1_landcover.proj
0 O elev_cm
B G NHDPIus Catchment Polygons (catchment) (catchment.shp) Role:SubBasin
B G State Soil (core3t .statsgo) (statsgo.shp) RoleiSoil
B ~ State Boundaries (core31 st) (st.shp) Role:State
B d Reach File. V1 (core31.rf1) (rfl.shp) Role.Hydrography
B B PCS3 (pcs3) (pcs3 shp) Role:Station
B C NAWQA Study Area Unit Boundaries (core31.nawqa) (nawqa.shp) Role:OtherBoundary
B ~ Land Use Index (core31.lulcndx) (lulcndx.shp)
B O Major Roads (core31.ftvards) (fhards.shp) Role Road
B O EPA Region Boundaries (core31.epa_reg) (epa_reg.shp) RolerOtherBoundary
B ~ Ecoregions (Level III) (core31.ecoreg) (ecoreg.shp) Role.OtherBoundary
B G County Names (core31 cntypt) (cntypt shp)
B Q County Boundaries (core31.cnty) (cnty.shp) Role County
B G Cataloging Unit Boundaries (core31.cat) (cat. shp) Role:SubBasin
B Q Bacteria Stations (core31 bac stat) (bac stat.shp) Role:Station
B E Accounting Unit Boundaries (core31.acc) (acc.shp) Role SubBasin
Wildlife
If wildlife are deemed to be a source of microbial contamination, they are assumed to be uniformly
distributed only in forested areas, so only density is required. If shedding from wildlife must be
considered, the FCProdRates.csv (Table 3) and WildlifeDensities.csv (Table 6) templates should be
updated. The user should not change column headings or names of the animal. If wildlife is not an
important source of microbes, all values in WildlifeDensities.csv template should be zeroed out.
Urban Built-up Areas
If Urban built-up areas are considered significant sources of microbial contamination, the
FCProdRates.csv template (Table 3) must be updated for roads (Road), commercial property
(Commercial), single-family-low-density residence (SingleFamilyLowDensity), single-family-high-density
residence (SingleFamilyHighDensity), and multi-family residential area (MultifamilyResidential). If they
are not, loading rates associated with these parameters in the FCProdRates.csv template should be
zeroed out (Table 3). The user should not change column headings or row labels.
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Table 3. FCProdRates.csv template and example production rate data. [Gray signifies loadings from
domestic animals and wildlife. Blue signifies
oadings from urbanized built-u
Source
Value
Units
DairyCow
1.01E+11
CountPerAnimalPerDay
BeefCow
1.04E+11
CountPerAnimalPerDay
Hog
1.08E+10
CountPerAnimalPerDay
Sheep
1.20E+10
CountPerAnimalPerDay
Horse
4.20E+08
CountPerAnimalPerDay
Chicken
1.36E+08
CountPerAnimalPerDay
Turkey
9.30E+07
CountPerAnimalPerDay
Duck
2.43E+09
CountPerAnimalPerDay
Goose
4.90E+10
CountPerAnimalPerDay
Deer
5.00E+08
CountPerAnimalPerDay
Beaver
2.50E+08
CountPerAnimalPerDay
Raccoon
1.25E+08
CountPerAnimalPerDay
Dog
4.09E+09
CountPerAnimalPerDay
OtherAgAnimal
0.00E+00
CountPerAnimalPerDay
OtherWildlife
0.00E+00
CountPerAnimalPerDay
Road
2.00E+05
CountPerAcrePerDay
Commercial
6.21E+06
CountPerAcrePerDay
SingleFamilyLowDensity
1.03E+07
CountPerAcrePerDay
SingleFamilyHighDensity
1.66E+07
CountPerAcrePerDay
MultifamilyResidential
2.33E+07
CountPerAcrePerDay
Microbial Die-off
Die-off (i.e., inactivation) rates are allowed to vary by month for the microbe of interest. Because only
one microbe is assessed at a time, die-off rates may need to be updated each time the microbe of
interest changes. An example of monthly microbial first-order die-off rate constants is presented in
Table 7 (MonthlyFirstOrderDieOffRates.csv). If there are no microbial loadings, having values in the file
will not affect the results. The user should not change column headings or row labels.
Point Sources
If point sources are located within the watershed, then PointSourceLL.csv and PointSourceData.csv
templates should be used, as illustrated in Tables 8 and 9, respectively. Publicly Owned Treatment
Works (POTWs) and Waste Water Treatment Plants (WWTPs) are typically associated with these
locations. Point sources are assumed to be directly discharged to the river/stream. Their locations
should be reported using the PointSourceLL.csv template which captures the Latitude-Longitude
location of each point source, along with a point-source identifier. If point source IDs are reported in the
PointSourceLL.csv, the user must have the same point source IDs in the PointSourceData.csv file. Users
should only change the values, not column headings. Single, annual-average flows, and microbial and
chemical loading rates are associated with each location and reported in the PointSourceData.csv
9

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template (Table 9) and only represent a place holder within the WDM file within BASINS. Actual point
source data must replace these values for a site-specific assessment.
Table 4. GrazingDays.csv template and example data
Month
BeefCattleGrazingDays
HorseGrazingDays
SheepGrazingDays
OtherAgAnimalGrazingDays
FractionOfTimeBeefCattlelnStreams
i
January
0
3.1
31
0
0
February
0
2.8
28
0
0
March
0
3
31
0
0
April
30
27
30
0
0.33
May
31
27.9
31
0
0.33
June
30
27
30
0
0.5
July
31
27.9
31
0
0.5
August
31
27.9
31
0
0.5
September
30
27
30
0
0.33
October
31
27.9
31
0
0.33
November
30
27
30
0
0.17
December
0
3.1
31
0
0
Table 5. ManureApplication.csv template anc
example data













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c
ManureType
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c
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(J
oj
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C
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FebFractionApplied
MarFractionApplied
AprFractionApplied
MayFractionApplied
JunFractionApplied
JulFractionApplied
AugFractionApplied
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0)
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CO
OctFractionAppied
NovFractionApplied
DecFractionapplied
"a
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Table 6. WildlifeDensities.csv template and example data
Animal
Density PerSqMile_Cropland
Density PerSqMile_Pasture
Density PerSqMile_Forest
Density PerSqMile_Builtup
Duck
0
0
0
0
Goose
0
0
0
0
Deer
5
5
5
0
Beaver
0
0
0
0
Raccoon
0
0
0
0
OtherWildlife
0
0
0
0
Table 7. MonthlyFirstOrderDieOffRateConstants.csv template and example data
Month
DieOffRateContant
January
0.36
February
0.36
March
0.36
April
0.51
May
0.51
June
0.51
July
0.51
August
0.51
September
0.51
October
0.36
November
0.36
December
0.36
Table 8. PointSourceLL.csv template for two point sources
Latitude
Longitude
PtSrcId
44.112
-88.256
PT001
44.06
-88.191
PT002
11
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Table 9. Example PointSourceData.csv template for two point sources with flow, microbes, and
chemicals
PtSrcId
FacName
Load
Parm
PT001
PointSourcel
1
FLOW
PT001
PointSourcel
1000
Microbes
PT001
PointSourcel
5
Diazinon
PT002
PointSource2
2
FLOW
PT002
PointSource2
2000
Microbes
PT002
PointSource2
4
Diazinon
If the user only wants to assess microbes, not chemicals, the file is modified by removing the rows for
chemicals in a manner similar to the example in Table 10. For chemicals only, the table is modified
similarly by eliminating the rows for microbes. Likewise, if there is only one point source, rows related to
the other point sources are removed. Also, multiple point sources can be identified, as illustrated in
Tables 11 and 12.
If the default data, as represented by the Latitude-Longitude pairs (Table 8), are outside the watershed
boundary, these data will not be assigned to any location within the watershed; hence, no modifications
are necessary to the PointSourceLL.csv or PointSourceData.csv default templates. If the default Latitude-
Longitude pairs (Table 8) are inside the watershed boundary (and they should not be), the Latitude-
Longitude pairs can be changed to locations outside the watershed boundary (e.g., zero out the
Latitude-Longitude pair).
Table 10. Example PointSourceData.csv template for two point sources with flow and microbes
PtSrcId
FacName
Load
Parm
PT001
PointSourcel
1
FLOW
PT001
PointSourcel
1000
Microbes
PT002
PointSource2
2
FLOW
PT002
PointSource2
2000
Microbes
Table 11. Example PointSourceLL.csv template for a single point source
Latitude
Longitude
PtSrcId
44.112
-88.256
PT001
Table 12. Example PointSourceData.csv template for a single point source with flow and microbes
PtSrcId
FacName
Load
Parm
PT001
PointSourcel
1
FLOW
PT001
PointSourcel
1000
Microbes
PT001
PointSourcel
5
Diazinon
12
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Septic Systems
If septic systems are located on the watershed, the SepticsLL.csv and SepticDataWatershed.csv
templates should be used, as illustrated in Tables 13 and 14, respectively. Their locations should be
reported using the SepticsLL.csv template which captures the Latitude-Longitude location of each.
Assuming each farm in the Manitowoc River basin contains one, locations of septics are illustrated by
Figure 2. Information supporting septic releases is reported in the SepticDataWatershed.csv template
(Table 14); these data represent the watershed as a whole - that is, the same average usage rate, failure
and overcharge rates, and microbial densities are applied to each septic location. All septics within each
subwatershed are combined to represent a single loading to the respective watershed stream segment.
At least one Latitude-Longitude pair must be identified, but if not relevant, enter zeros in for the
Latitude and Longitude in the SepticsLL.csv template (Table 13). If zeros are identified for the Latitude-
Longitude pair, it is not necessary to zero out the values in SepticsDataWatershed.csv Template (Table
14) since these data will not be assigned to any location in the watershed. Users should not change
column headings.
Intermediate Watershed Locations
Sampling and monitoring traditionally occur at locations with easy access, not locations that are most
advantageous for modeling. Software-based automated delineation programs used for watershed
modeling typically divide a watershed into subwatersheds without regard to sampling/monitoring
locations. Hence, locations where simulation results are available do not necessarily correspond to the
sampling/monitoring locations.
For example, two inter-watershed locations of interest (red dots) within a delineated watershed where
the subwatersheds are outlined are presented in Figure 3; however, the automated delineation (thin
black lines) does not coincide with the sampling/monitoring locations (see Figure 3a) and these data
cannot be used in model calibration. In this case, the user must manually delineate the watershed to
ensure subwatershed boundaries coincide with the sampling/monitoring locations.
The SDMProjectBuilder automatically delineates the watershed so that the subwatershed boundaries
coincide with intermediate watershed locations of interest. Sampling/monitoring locations were
identified prior to delineating into subwatersheds, and they were factored into the delineation process
(Figure 3b). Subwatershed boundaries, therefore, coincide with the sampling/monitoring locations and
no manual delineation is required. Two additional files associated with intermediate points of interest
(output locations and boundary conditions) request Latitude and Longitude locations within the
SDMProjectBuilder. Each is discussed below.
Output Locations
Output locations are intermediate points, where the user would like the watershed model to produce
simulation results, and only exist at subwatershed boundaries (see Figure 3b). As noted earlier, by
ensuring that simulation results coincide with sampling/monitoring locations, they can be directly
compared to sampling/monitoring data and can help calibrate the model for subwatersheds upstream
from this location. The OutputPoints.csv template (Table 15) captures output Latitude-Longitude
locations. When modifying the csv file, users may identify more than one location, but should not
13
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change column headings. At least one Latitude-Longitude pair must be identified, and if not relevant,
enter zeros in for each Latitude and Longitude in the OutputPoints.csv template (Table 15).
Table 13. SepticsLL.csv template
Latitude
Longitude
44.22582
-88.0305
44.2114
-88.0873
44.09547
-88.0263
44.23976
-88.0939
44.19051
-88.1283
44.22693
-88.1872
44.19139
-88.1327
44.18323
-88.146
44.22671
-88.1462
44.12401
-88.0751
44.2271
-88.2093
44.19682
-88.0229
44.1845
-88.1445
44.21851
-88.0042
44.12406
-88.0718
44.23874
-88.1834
44.17717
-88.0314
44.21836
-88.1342
• •
• •
• •
44.05756
-88.1512
44.08862
-88.1774
43.97918
-87.8456
44.30336
-88.1727
43.91199
-88.3076
44.11344
-87.8003
44.12612
-88.2568
Boundary Conditions
After a model has been calibrated at one output location or if data exist that provide necessary
boundary conditions, these data could be directly consumed by the watershed model without re-
running the simulation upstream of the boundary condition location. In essence, those subwatersheds
would be removed from the assessment and replaced by a file containing previously collected data or
calibration results; for example, a user-specified location (red dot) where known flow data exists is
illustrated by Figure 4a. As opposed to simulating that portion of the watershed upstream from this
14
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point (aqua region in Figure 4b), flow information at that location could be provided as the upstream
boundary condition in a file, eliminating the need to model the upstream portion (aqua region in Figure
4b).
Table 14. SepticsDataWatershec
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Table 15. OutputPoints.csv Template
Latitude
Longitude
44.065
-88.226
The BoundaryPoints.csv template (Table 16) captures Latitude-Longitude boundary locations. In the
SDMProjectBuilder, these are associated with an instream location, not an overland segment. When
modifying the csv file, users may identify more than one location but should not change column
headings. Currently, the SDMProjectBuilder only allows the user to identify the boundary condition
location - consuming boundary condition data has NOT been activated. At least one Latitude-Longitude
pair must be identified and if not relevant, enter zeros for each Latitude and Longitude in the
BoundaryPoints.csv template (Table 16).
15
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Figure 3. Delineated watershed (a) without considering intermediate points of interest to the user
within the watershed, and (b) considering intermediate points of interest
Figure 4. Example of using a boundary condition to identify a location where data are known: (a) red dot
symbolizes the boundary condition location on a watershed and (b) aqua region symbolizes the region
where known data would replace and modeling simulations.
Table 16. BoundaryPoints.csv template
Latitude
Longitude
44.02731
-88.1643
16
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NAVIGATING THE SDMProjectBuilderTO IDENTIFY A HUC-8
Whelari et al. (2015c) describe navigation of the SDMProjectBuilder and how to identify a watershed of
interest by providing step-by-step instructions to
Identify a New project ("New SDM Project")
7T&PM Project BwMwl
1 File
New SOM Project
I ~ ~ *
I l*9«'

1 >j
Options

i


• Navigate through the GIS with the Navigation Helper ("Nav Helper") to identify the relevant 8-
digit HUC (HUC-8) of interest:
SDM Project Builde
SDMProjectBuilder | Extensions
N
M Project
Nav Helper
Import Local Data Files
Run Project Builder
Options
-;-r»TTroc"W
17
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IMPORTING LOCAL DATA FILES AS MAP LAYERS
Of the 12 default local data files, five report locations that can be imported and displayed as map layers
(i.e., AnimalLL.csv, BoundaryPointsLL.csv, GutputPointsLL.csv, PointSourceLL.csv, and SepticsLL.csv),
using the following procedure.
1. By clicking on "Import Local Data Files" under the SDMProjectBuilder tab,
pSDM Project Builder
.=151 xj
File
m
f'Legei
SDMProjectBuilder | Extensions
New SDM Project
Nav Helper
Import Local Data Files
Run Project Builder
Options
B" 121 HUC-8
O
Map
A
ilZl ds *1* 1
~	N
~	y
El l*j Counties
~

m mi
X:-9687650,33029 Y: 6434061,65565 X:-9687650,33029 Y: 6434061,65565
a screen will appear that allows the user to import 12 "Local Data Files" of which the five files listed
in the following screen identify specific Latitude-Longitude locations for domestic animals (e.g.,
farms), intermediate points (i.e., boundary conditions, output points), point sources (e.g., POTWs),
and septic systems.
Edit Local Data
Jn|xj
Local Data Files
Animal LL
HI
BoundaiyPointsLL
"I
OutputPointsLL

Point Source LL

SepticsLL
zl
Open File
Edit File
J
Start Adding Points
Delete Selected Point(s) on Hap |
Close File I
Close
18
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2.
To register the relevant local data files containing points of interest, choose "Open File" and wait
until the screen changes, then choose "Close File." For example: to register locations of domestic
animals, choose "AnimaILL," as illustrated below, then "Open File."

Edit Local Data
Local Data Files
AnimaILL
HI
Boundary Points LL
"1
Output Points LL

PointSourceLL
——J
	11
SepticsLL
Open File
Edit File
Start Adding Points
Delete Selected Points) on Map |	Close File |
|(^ D4EM Project Builder
The locations contained in the AnimalLL.csv file, found in the "LocalData" folder, will be registered
as a map layer, as illustrated below:
File D«M
! ~ ~ |i # |l @ E
~ ^ Map Layers
E 0 PointSourceLL
^10 AnimalL^^^k
B[5nu!3^r04030101
~
~ nhdflowline
Eisi
~
B 0 huc250d3
~
B O cnty
~
— In I x |
X: -9916268.56099064, Y: 5540068.49140714
19
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3. Choose the "Close File" button to exit the "AnimaILL" map layer registration.
Local Data Rles
BoundatyPointsLL
Output Points LL
PointSounceLL
SepticsLL	
0
Open Rle |
Edit Rle
Start Adding Points
Delete Selected Point(s) on Map
Close Rle
4. Repeat for the other relevant local data files: BoundaryPointsLL, OutputPointsLL, PointSourcesLL,
and SepticsLL,
5. When complete, click the "Close" button to exit the screen.
-!~! *1
Edit Local Data
Local Data Files
AnimaILL
BoundaryPointsLL
OutputPointsLL
PointSounceLL
SepticsLL
Open Rle
Edit File
J

Start Adding Points |
Delete Selected Point(s) on Map
Close
Close File
Although the software will allow the user to "Edit File", "Start Adding Points", and "Delete Selected
Point(s) on Map", these features have not been fully tested. It is recommended that the user directly
modify the csv files using tools such as Excel, Notepad, or Textpad.
20
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SPECIAL NOTES ON IMPORTING POINT SOURCE TIME SERIES DATA
This section discusses conditions for importing point source time series data through HSPF and BASINS,
replacing the default data illustrated in Tables 8 and 9. It is assumed that the reader is familiar with
SDMPB screens documented in various SDMPB tutorials (e.g., Whelan et al., 2015d). Whelan et al.
(2015e) provides a tutorial for importing point source time series for flow and microbial loadings.
For HSPF to correctly model microbial and/or chemical point source loadings, the following conditions
must be met:
1.	For microbes, the "Microbes" text box in the SDMProjectBuilder user interface (Figure 5) must
be checked. Because a chemical point source loading is different from a land-applied chemical
loading, the check box for "Land-Applied Chemical" is irrelevant (Figure 5).
2.	The text box must be checked for point sources in the HSPF "Point Sources" window, and "YES"
must be selected beside "MICROBES" in the "Details of POINT SOURCES (OBS)" section (Figure
6). To get to the HSPF "Point Sources" window, select "Functions" in the main HSPF menu bar,
then "Point Source Editor" (Figure 7). If chemicals are being assessed, then the chemical would
also have to have "Yes" by its name.
3.	PointSourceLL.csv default template must be updated with the correct Latitude-Longitude.
4.	The correct time series will have to be imported to the WDM file using BASINS.
If condition 1, 2, or 3 is NOT met, point sources will not be considered in the assessment.
Figure 5. Screen capture of the SDMProjectBuilder interface, indicating a microbial assessment will be
performed
] Build Frames SDM Project

t~ Parameters For Model Generation
w
|oT
1930
|2DD0
Minimum Catchment Size (square kilometers)
Minimum Flowline Length Odometers)
Ignore Landuse Areas Below Fraction
Simulation Start Year
Simulation End Year
P HSPF Output Interval: |Hourty
3
Snow: No Snow
rp Microbes!
r Land-Applied Chemical
Chemical Properties
I- SWAT SWAT 2005 Database | d:\devnotmw >
bin\debugVnodels\SWAP\Databases\swat 2QQ5.mdb
Cancel
Previous
Next
21
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Figure 6. HSPF Point Sources window
I WinHSPF - Point Sources

© Add Point Source
r Selectf Deselect All
0*
Details of P0INTS0URCE3 (OBS)
In Use | Reach
	| Pollutant | Target Member
RCHRES 6 - Killsnake River FLOW IVOLI water
RCHRES 6 - Killsnake River MICROBES IDQAL(1) I dis+
Q Hide Details |
Figure 7. Main HSPF screen highlighting "Functions" on the menu bar
jif Hydrological Simulation Program - Fortran (HSPF): 04Q301010406.uci
E)
File Edit QFunctions^ Help	It'1 M © S p" & H 13 -3 I ^ %
Water/Wetlands
Urban
Barren or Mining
Fr*r#^t
I.
RCHRES5
RCHRES1
...I
RCHRES3
RCHRES2
Land Use
Reaches
Implnd (.Acres)
Perlnd (Acres)
Total (.Acres)
Modifications to the PointSourceData.csv template update only a single annual-average value for flow,
and microbial and chemical loading rates. Default values contained in the file are very small and typically
will not impact any simulations, even if they are incorrectly included in the assessment. The file should
not be directly modified to include site-specific, time-series data. The actual time series of flows, and
microbial and chemical loading rates for each location can only be recorded through the HSPF user
interface. A tutorial has been developed to show the user how to import point sources into an
assessment; see Whelan et al., (2015e).
22
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DISCLAIMER
This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and
approved for publication.
REFERENCES
Garnett, L.W. 2012. 5 High density housing concepts.  (Last accessed 11.9.2015).
Whelan, G., K. Kim, K. Wolfe, R. Parmar, M. Galvin. 2015a. Quantitative Microbial Risk Assessment
Tutorial: Installation of Software for Watershed Modeling in Support of QMRA. EPA/600/B-15/276. U.S.
Environmental Protection Agency, National Exposure Research Laboratory, Athens, GA.
Whelan, G., R. Parmar, G.F. Laniak. 2015b. Microbial Source Module (MSM): Documenting the Science
and Software for Discovery, Evaluation, and Integration. EPA/600/B-15/315. U.S. Environmental
Protection Agency, Athens, GA.
Whelan, G., K. Kim, K. Wolfe, R. Parmar, M. Galvin, M. Molina, R. Zepp. 2015c. Navigate the SDMPB and
Identify an 8-Digit HUC of Interest. EPA/600/B-15/273. U.S. Environmental Protection Agency, Athens,
GA.
Whelan, G., K. Kim, R. Parmar, K. Wolfe, M. Galvin, M. Gray, P. Duda, M. Molina, R. Zepp. 2015d.
Quantitative Microbial Risk Assessment Tutorial: Land-applied Microbial Loadings within a 12-Digit HUC.
EPA/600/B-15/298. U.S. Environmental Protection Agency, Athens, GA.
Whelan, G., K. Wolfe, R. Parmar, M. Galvin, M. Molina, R. Zepp, P. Duda, M. Gray. 2015e. Quantitative
Microbial Risk Assessment Tutorial: Point Source and Land-applied Microbial Loadings within a 12-Digit
HUC. U.S. Environmental Protection Agency, Athens, GA.
Whelan, G., K. Kim, K. Wolfe, R. Parmar, M. Galvin, M. Molina, R. Zepp, P. Duda, M. Gray. 2015f.
Quantitative Microbial Risk Assessment Tutorial: Pour Point Analysis of Land-applied Microbial Loadings
and Comparison of Simulated and Gaging Station Results. EPA/600/B-15/290. U.S. Environmental
Protection Agency, Athens, GA.
Wikipedia. 2015a. Single-family detached home.  (Last accessed 11.9.2015).
Wikipedia. 2015b. 
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