inSALMO is free software published under the GNU General Public License. Software and images © 2011-2014 Lang, Railsback & Assoc.

InSALMO and inSALMO-FA

InSALMO is an individual-based model of freshwater life stages (spawning through outmigration) of salmon, and inSALMO-FA is a version that includes facultative anadromous salmonids such as steelhead. The Sacramento Fish and Wildlife Service's Instream Flow division assisted the US Bureau of Reclamation and USFWS Bay Delta Field office in the development of these models and their application to Clear Creek.

Primary Downloads

The following table provides the primary products. Right-click on the links in the first column to download files.



File name (right-click to download) Description File size Last updated

inSALMO_1-5_ModelDescr.pdf

T1-Validation_FinalReport.pdf

T2-SpaceEffects_FinalReport.pdf

T3-SpatialRes_FinalReport.pdf

T7-SteelheadModel.pdf

Final products for the 2012-2013 project funded by USFWS: Updated model description, report on Task 1 (validation of the model to Clear Creek data), report on Task 2 (effects of spatial extent—number of simulated reaches), report on Task 3 (effects of spatial resolution—cell size), and description of inSALMO-FA.

823 KB

2682 KB

250 KB

1431 KB

502 KB

27 Sept 2013

06 Sept 2013

06 June 2013

27 Sept 2013

30 Sept 2013

RailsbackEtAl_NAJFM2013.pdf

RailsbackEtAl_CJFAS-2014.pdf

RailsbackEtAl_CJFAS_SM.pdf

Publications based on the project:

Railsback, S. F., M. Gard, B. C. Harvey, J. L. White, and J. K. H. Zimmerman. 2013. Contrast of degraded and restored stream habitat using an individual-based salmon model. North American Journal of Fisheries Management 33:384-399.

Railsback, S. F., B. C. Harvey, and J. L. White. 2014. Facultative anadromy in salmonids: linking habitat, individual life history decisions, and population-level consequences. Canadian Journal of Fisheries and Aquatic Sciences 71:1270-1278. (Supplementary Material in separate file is a complete description of inSALMO-FA.)

1020 KB

1338 KB

1060 KB

19 Mar 2013

01 Aug 2014

14 Apr 2014

inSALMO-Version1-0_2012-05-18.pdf

Complete report on the 2011-2012 project funded by US Bureau of Recalamation, documenting the project purpose, the pilot application to Clear Creek, example decision-support applications, an example "limiting factors" analysis, and an analysis of remaining model development and research needs. Appendices (which are also help files in the model software) are: (A) a complete description of the model, (B) the software guide, (C) the graphical user interface guide, and (D) a guide to the Limiting Factors Tool. These appendices are superceded by the help files packaged with inSALMO’s software.

3.02 MB (303 pages)

18 May 2012

inSALMO_1-5.zip

inSALMO-FA_1-5.zip

The inSALMO 1.5 and inSALMO-FA 1.5 software packages, in their graphical user interfaces for Windows. The packages include complete input for Clear Creek. See instructions below for installing the software.

33.4 MB

30.9 MB

9 Oct 2013

9 Oct 2013

Instructions for installing inSALMO 1.0 in Windows

The inSALMO software and graphical user interface are packaged for Windows users as a ZIP archive file. To install the model and interface:

  1. Download the inSALMO zip file from the above table. Store it anyplace.
  2. Unzip the inSALMO zip file into a convenient directory where you have permission to write files. This will create a new subdirectory tree called inSALMO which will contain all the model files. For example, the zip file can be extracted to your My Documents directory.
  3. Using the Windows Explorer, navigate to the \inSALMO\GUI subdirectory. If you extracted the zip file to My Documents, this directory will be My Documents\inSALMO\GUI.
  4. In the \inSALMO\GUI directory, right-click on the file inSALMO.exe. Select "Create a shortcut", which will create a new shortcut file with the inSALMO icon: inSALMO Icon
  5. Drag the new shortcut file to your desktop. Click on it to start the graphical interface.

Supplementary Downloads

The following table provides files not needed by normal inSALMO users. The last five rows provide files that document tests of various parts of the code. (Other parts of inSALMO's code were copied from the inSTREAM trout model, and thoroughly tested previously.)

File name Description File size Last updated
ClearCrkProjWithUpperIsolation.zip

Zip archive of an inSALMO project (a directory of input files) that includes a third reach on Clear Creek: Upper Isolation. This reach was developed from USFWS instream flow study data, as documented in Sect. 7 of the project report.

330 KB 31 Jan 2012
insalmo1-2_2012-05-18.tgz

Code files for the inSALMO model, without the graphical interface. The model code is provided for users who wish to install and use it outside the graphical interface (e.g., so they can use it in 64-bit Linux for better performance), or to modify and re-compile it. Tar-gzip format. Code is in Objective-C for use with the Swarm simulation system. Code compiles with either the gcc or MinGW compiler. The standard input set for Clear Creek is included.

461 KB 18 May 2012
inSALMO-GUI_1-0-1.zip

Code files for the inSALMO graphical user interface (not including the model itself). Zip format. This archive includes the Java code for the GUI (including the Limiting Factors Tool), plus all the GUI's input that defines default parameter values, LFT parameters, projects, etc.

12.6 MB 13 Oct 2011
FlowImportTool.xlsx

An Excel workbook that converts simulated monthly mean Whiskeytown Dam releases into daily flow input for inSALMO. The workbook uses historic tributary inflows to synthesize daily flow values that retain natural sub-monthly flow variability.

2.3 MB 10 Oct 2011
3A-Z&V Comparisons.110516.xlsx
3C-Z&V Comparisons.110516.xlsx
Two Excel workbook files testing code for hydraulic habitat (depth and velocity) simulations for the 3A and 3C reaches at Clear Creek. 92 KB 90 KB 17 May 2011
EggEmergenceCheck.xlsx

Excel workbook file documenting tests of code for spawner fecundity and number of eggs emerging as fry.

31 KB 8 July 2011
FoodAvailCheck.110518.xlsx

Excel workbook documenting tests of code for food depletion and availability, including effects of superindividuals.

36.1 MB 20 May 2011
Move_Test_Out.xlsx

Excel file testing code for many habitat selection, energetic, and spawning functions.

17.6 MB 2 June 2011
SpawnCheck.xlsx

Excel file testing code for when adults spawn.

629 KB 31 May 2011

For information contact: Steve Railsback

Click here for additional information on individual-based modeling and ecology affiliated with Humboldt State University's Department of Mathematics.