Exhibit 99.1

Simulations Plus, Inc.
NASDAQ: SLP
Third Quarter Fiscal Year 2009
Conference Call
July 16, 2009

Introduction and Welcome

•Introduction and Welcome

•Agenda

–Third Quarter FY 2009 (3QFY09)
Financial Summary

–Progress in Business Units

–Strategy Going Forward

–Questions and Answers

With the exception of historical information, the matters discussed in
this presentation are forward looking statements that involve a number
of risks and uncertainties. The actual results of the Company could
differ significantly from those statements. Factors that could cause or
contribute to such differences include, but are not limited to: continuing
demand for the Company’s products; competitive factors; the
Company’s ability to finance future growth; the Company’s ability to
produce and market new products in a timely fashion; the Company’s
ability to continue to attract and retain skilled personnel; the Company’s
ability to identify, evaluate, and close suitable acquisitions; and the
Company’s ability to sustain or improve current levels of productivity.
Further information on the Company’s risk factors is contained in the
Company’s quarterly and annual reports and filed with the Securities
and Exchange Commission.

Safe Harbor Statement Under the
Private Securities Litigation Reform Act
of 1995

3QFY09 (3 months) Financial Summary

•Gross revenues = $2.713 MM (down 8.6% from 3QFY08)

–Pharmaceutical software and services = $1.985 MM (up 0.5% from $1.975 MM in 3QFY08)

–Words+ subsidiary = $728,000 (down 26.7% from $994,000 3QFY08)

•SG&A = $989,000 (up 5.0% from $942,000 in 3QFY08)

–Increased spending for marketing and sales (trade shows, travel, etc.) is major factor

•R&D Expense = $334,000 (up 50.4% from $222,000 from 3QFY08)

–Greater time on funded collaborations (4 at present), less capitalized software development

•Income Before Income Taxes = $888,000 (down 25.3% from $1,188,000 in 3QFY08)

–Increased investments in marketing and sales, R&D costs, and less gross profit.

–~$90,000 greater write-off of old Words+ invoices - conservative estimate - still working on
them. Additional funding staff & special software have improved short-term collections.

•Net Income = $569,000 (down 24.4% from $753,000 in 3QFY08)

–~$40,000 increase in income taxes

•EPS = $0.03/FD share (down $0.01 from $0.04/FD share in 3QFY08)

–Growth and profitability continue in spite of global economic crisis

•Cash = $7.373 MM (up $1.387 MM or 23.2% from $5.986 MM in 3QFY08)

–Cash increases even with share repurchase program

•Shareholders’ Equity = $10.936 MM (up 12.9% from $9.960 MM in 3QFY08)

3QFY09 (9 months) Financial Summary

•Gross revenues = $7.303 MM (up 2.4% from 9 months FY08)

–Pharmaceutical software and services = $0.231 MM (up 4.7% from $4.963 MM in 9 months
FY08)

–Words+ subsidiary = $2.110 MM (down 2.7% from $2.169 MM in 9 months FY08)

•SG&A = $2.929 MM (up 8.3% from $2.705 MM in 9 months FY08)

–Increased spending for marketing and sales (trade shows, travel, etc.) is major factor

•R&D Expense = $996,000 (up 42.2% from $700,000 in 9 months FY08)

–Greater time on funded collaborations (4 at present), less capitalized software development

•Income Before Income Taxes = $1.900 MM (down 17.2% from $2.295 MM in 9
months FY08)

–Increased investments in marketing and sales, R&D costs, and less gross profit.

–~$220,000 greater write-off of old Words+ invoices - conservative estimate - still working on
them. Additional funding staff & special software have improved short-term collections.

•Net Income = $1.249 MM (down 20.0% from $1.561 MM in 9 months FY08)

–Slightly higher estimated tax provision rate (34.3% in FY09 vs. 32.2% in FY08 at the end of 9
months operation.

•EPS = $0.07/FD share (down $0.02 from $0.09/FD share in 9 months FY08)

–Growth and profitability continue in spite of global economic crisis

•Cash = $7.373 MM (up $1.387 MM or 23.2% from $5.986 MM in 3QFY08)

–Cash increases even with share repurchase program

•Shareholders’ Equity = $10.936 MM (up 12.9% from $9.960 MM in 3QFY08)

Share Repurchase Program

•Board of directors authorized share repurchase program for up to
$2.5 million from October 2008 through October 2009

•During 3QFY09, 172,978 shares were bought back at average
price of about $1.02/share.As of July 10, over 648,000 shares
bought back at average price per share of about $1.14.

–Over $1.7 MM remains authorized for additional repurchases

–Plan is to continue repurchases - goal to buy back maximum number of
shares, not to support a particular stock price

•Share repurchases are subject to Safe Harbor restrictions:

–Number of shares that can be bought back per day in non-block trades is
25% of average daily trading volume for previous 4 weeks

–Block trades require approximately 40,000 shares per block

–Cannot have block and non-block purchases on the same day

–Can only purchase on an up-tick, etc.

–Cannot have repurchases when insiders are trading

•Plan is to continue repurchase for the foreseeable future

Progress - 1

•ADMET Predictor™

–Program was divided into modules with the last release

•Requested by a number of smaller potential customers to reduce costs -
appears to be a successful pricing strategy

–New Dose Optimization Module determines dose amount needed for
different new molecules based on mini-GastroPlus simulation

–New toxicity models: five new liver toxicity models

–New metabolism models: seven new enzymes included

–Powerful expanded graphics capability allows users to “see” in up to 8
dimensions using X, Y, Z, size, color, shape, texture, and label for each
data point. Sliders can filter the data in any of hundreds of molecular
descriptors and other properties.

–Version 4.0 has just been finalized with all new retrained models,
additional toxicity models, and user convenience features - expect formal
release next week.

–Awarded $525,000 SBIR Phase II: work began in 4th quarter - no
revenues were recognized in Q3

Miner3D™ Graphics
in ADMET Predictor 4.0

Progress - 2

•ClassPharmer™

–Continuing to enhance ability of ClassPharmer in data mining and de
Novo molecule design (design of new molecules)

–Presentation at a conference in London showing the power of
ClassPharmer combined with ADMET Predictor for the automatic
generation and screening of new virtual molecules led to a number of
leads, including an on-site presentation at a large pharmaceutical
company in Switzerland. After the meeting, they said they are now
planning a formal evaluation for this year.

–New “scaffold hopping” capability in beta test - allows chemists to
change the core (or any portion) of a molecule while maintaining
other features and the bond distances between them.

–New method to generate molecular transformations (like reactions)
from Pair SAR results to design better molecules.

ClassPharmer Pair SAR (“Activity Cliffs”)
for hERG Toxicity

Progress - 3

•DDDPlus™

–Sales increasing steadily, with customers now in U.S., Europe, Japan, and
India, including two licenses at the FDA

–Version 3.0 released during Q3 - major update

–Remains the only tool of its kind

•GastroPlus™

–Development of Drug-drug Interaction module progressing very well
under funded collaboration - initial capability in beta test at Roche

–Development of ocular delivery capability under a funded collaboration
with a top 3 pharmaceutical company also progressing well - simulation
is running

–Development of a nasal-pulmonary delivery module is in early stages
under funded collaboration with major pharmaceutical company

–Consulting contracts continue to come in to assist pharmaceutical
companies worldwide in analyzing preclinical and clinical data with
GastroPlus

Simulates laboratory dissolution experiments

DDDPlus 3.0

GastroPlus Ocular Delivery - Funded
Collaboration

GastroPlus Pulmonary Delivery

Progress - 4

•Words+ subsidiary

–General economy appears to be affecting this business -
many states are struggling, and a large percentage of our
sales come from 3rd-party sources (Medicaid, Medicare,
schools, state vocational rehabilitation programs, etc.)

–New Conversa™ communication device selling well

–Full-time national sales manager working to improve
marketing and sales activities and dealer relationships

–Two new employee sales reps added in California

Miscellaneous

•Potential acquisition we were working on for a number of months did not go
through - seller decided to go with another buyer. No news if that deal has been
concluded. Potential remains to acquire software part of the business if the new
buyer is not interested in it.

•Due diligence initiated on two new acquisition possibilities for the
pharmaceutical side of the business.

•Director of Business Development hired and has hit the ground running!

•Two new hires will be starting in August and September. Both recent Ph.D.
graduates with excellent related backgrounds.

•Advertising for additional scientists to enhance our Life Sciences team. Study
contract requests are coming in at a significantly faster pace.Customers range
from small to mid-size companies all the way to top 5 pharmaceutical
companies.

Strategy Going Forward

•Continue to expand product line and services

–Pharmaceutical software and services

•Expand Life Sciences team by several scientists

–For new product development as identified in corporate strategic planning

–To increase capacity to conduct consulting studies and funded collaborations

•Seek and complete strategic acquisitions

–Goal is to add both new products & services as well as additional scientific staff

•Examine additional SBIR opportunities

–Words+ subsidiary

•Continue product improvements and more aggressive marketing and sales

•Added staff to process prior authorizations and accounts receivable more quickly -
collecting old receivables from state Medicaid agencies

•Look for SBIR funding opportunities that fit our expertise

•Continue our expanded marketing and sales activities - increasing number
of conferences and meetings worldwide - lead list is growing

–China appears to be significant potential market for pharmaceutical business

–Environmental toxicology area outside of the pharmaceutical industry appears
also be large potential new market

Summary

•Simulations Plus financial strength continues

–Excellent cash position that continues to grow

–No debt

–Share repurchase is gradually reducing number of shares outstanding without
major impact to cash position

•Decent third quarter - not outstanding, but in this economy, healthy

–Pharmaceutical software and services revenues up slightly from 3QFY08 in
spite of one large order ($124,000) slipping into the 4th quarter by a few days

•Focus on maintaining best-in-class position in product quality and superior
customer service

•Acquisitions in the works (although there can be no assurance that any will
be completed).

•Slides available by e-mail on request through info@simulations-plus.com

Impact Of Economic Environment

•Budgets

•Greater Tightening of R&D Budgets

•Diminished Spending On Conference and Symposium Attendance By Prospect Organizations

•Spending

•Greater Justification Required For Any Type Of Spending

•Organizations implementing Spending Increase Caps Of 4-7%

•Approvals

•Greater Number Of Management Layers Required To Approve Spending

•Authorization Approval Limits Are Being Lowered

•Decision Making

•Greater Amount Of Time Taken To Make Spending Decisions

•Purchasing Department Buyers Involved In Smaller And Smaller Sales

•Software Usage Audits

•Lengthy Audits Being Required To Justify License Renewal Purchases

•Making Due With What We Have

•Mindset Is Slowing License Expansions In Some Organizations

•Personnel Changes

•Heavy Layoffs Of Power Users In Customer Organizations Negatively Impacts License
Renewals

•Mergers/Acquisitions

•Stalls Software Purchases Due To Uncertainty Of The Needs Of The New Organization

Questions?