PharmaExpert - Pharmacology Software

PharmaExpert analyzes the relationships between biological activities, the interactions of drugs and the multiple targeting actions of chemical compounds. As a pharmacological knowledge-based tool, it provides in silico screening of compounds using PASS prediction results.

Details
Key features of PharmaExpert:
• Mechanism-effect relationship (MER) base, manually curated by experts, contains 11,049 mechanism-effect relationships
• Selection of compounds with required therapeutic but without side effects
• Comparative analysis of compounds with similar structures
• Selection of compounds with multiple mechanisms of action
• Analysis of drug-drug interactions with regard to their pharmacokinetic, pharmacodynamic and adverse effects

PharmaExpert is an addition to the PASS (Prediction of Activity Spectra for Substances) tool. It provides a comfortable solution for data mining of the PASS prediction results to find the best drug-like candidates from a set of compounds. The core of the program is a mechanism-effect relationship (MER) base, manually curated by experts, which is used to determine cause-effect relationships for the compounds. Like PASS, the software runs under Windows.

PharmaExpert has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

A free demo version, as well as further information, is available upon request.

Software Link: PharmaExpert - Pharmacology Software

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Metabase - laboratory data management software

Metabase is a laboratory data management software system designed specifically to meet the needs of laboratories conducting ADME metabolism, pharmacokinetics, and toxicokinetics studies. Starting with the generation of a sample list for an entire study, Metabase serves as the basic tool to acquire, organize, manage, calculate, store, and report study results. Key features of the program are its clear organization (which follow standard laboratory workflow procedures), its flexible and powerful data handling, its ease of use, and its integration with other productivity software. The flow sheet on the right illustrates the overall process of using Metabase as your primary data handling and management system.

Metabase is a practical, low cost, user-friendly, laboratory-oriented tool. The program is based on Microsoft Excel® and can be easily custom tailored to fit each client's work place or modified to meet changing needs and requirements. And to make sure that it does the job the right way, it was designed and operated in radio-analytical metabolism research laboratories.

Metabase comes as a turn-key system for radio-analytical sample processing and liquid scintillation counting data, but it can be custom modified for other analytical methods. Metabase is designed to meet GLP guidelines and comply with FDA, EPA, EEC software development and validation requirements. The system is provided with complete system life-cycle documentation. Test files are supplied for use in validation. Metabase is a cost-effective solution for comprehensive management of metabolism information in a well organized, flexible, and user-oriented manner.

Benefits

Specifically designed for sample handling of ADME metabolism and pharmacokinetic studies.
Excel-based software providing wide flexibility in a familiar spreadsheet environment.
An exceptionally affordable LIMS system for radioanalytical lab.
Helps you define, collect, manage, calculate, and report entire study protocols.

Features

Excel-based for Reliable Performance

Metabase is based on Microsoft Excel® and can run in any version of Excel in versions of Microsoft Windows. Excel provides a familiar working environment for using Metabase. Additionally, Metabase can take full advantage of all the functions, features and power of Excel.

Flexibility

The need for flexibility is an overriding requirement for any metabolism data handling system. No two studies are exactly alike. Therefore, every function of Metabase is designed with flexibility in mind. Added to this, the "open architecture" afforded by Excel spreadsheet operations allows user control over such features as formatting and appearance, significant figures, and exporting of results. Input functions and calculations can be modified or added, as needed.

Lab Smart

Metabase is a "lab smart" tool. It was developed by researchers with extensive experience in metabolism studies and is designed to provide assistance through all phases of a typical metabolism study.

Protocol and Study Designs

Metabase can handle any type of study design, whether the study involves serial sampling of individual animals, time-based composites from groups of animals, multiple dose levels, or even variable specific activities. Metabase helps the user set up a clear one-page overview of the study design and sampling strategy and uses this to develop a master sample information database.

Variable Dose Methods

Metabase supports dose computations based on individual dose measurements or nominal dose amounts per group. Additionally, different specific activities can be used for each dose group, such as employed in EPA's guidelines for dermal absorption studies.

Automated Data Entry

No hand entries of data. Metabase automatically reads data files obtained from a liquid scintillation counter or it can be directly connected for on-line data transfer. Similarly, Metabase automatically prepares a Sample Processing spreadsheet that can be linked to auto-balances for direct transfer of weight measurements.

Sample Processing

Metabase incorporates unique features to help you manage both your samples and your data from collection to counting. Special algorithms summarize laboratory processes and provide a consistent method for gathering and processing quantitative measurements, regardless of the number and complexity of sample processing procedures. Automated balances and robot-controlled processing stations can serve as data inputs. Volumetric measurements can be gathered electronically or entered directly into electronic forms.

Adaptable and Expandable

The primary design is to provide acquisition of LSC and auto-balance or robot-processing data. However, Metabase can be extended or modified to acquire quantitative results from other analytical instruments. In fact, due to its modular nature, the program can be customized to provide data management support for other disciplines besides metabolism.

High Throughput

There are practically no limits to the number of study animals, sample types, or time points that can be assembled in a single study. A single data file can handle approximately 16,000 records, and multiple files can be used in a study

Radioactivity Calculations

A built-in calculation module provides initial dose calculations such as the amount of total dose and radioactivity required, the limit of detection and analytical sensitivity for a given specific activity, and other useful values.

Pharmacokinetics

Metabase results can be passed directly to PK Solutions, Summit's powerful pharmacokinetics data analysis program. This program generates all commonly reported PK parameters from blood levels obtained after single, multiple, and infusion dose regimens.

Report Generation

Automatically prepares data tables with appendix and report quality formats, including color, if desired. User-selectable output choices and data arrangement. Metabase data outputs can be custom tailored for specific analysis routines or for advanced document preparation.

Custom Design

Metabase is designed to fulfill core functions associated with metabolism sample management and data acquisition, analysis and reporting functions. Typical installation in the client laboratory involves custom modifications to insure that the program fits with individual client procedures, needs, and requirements.

QA and GLP Compliant

Metabase is designed to comply with GLP guidelines and to facilitate QA data reviews. In addition to built-in data protection and automatic audit trails, the laboratory may choose among several alternatives for managing authorized entry and use.

SDLC Documentation

Metabase comes with a complete system development life cycle documentation package to make validation a breeze. The minimum validation documentation set includes Requirements Analysis, System Design Specifications, Version History, Source Code, User Manual, Test Procedures, and Test Files. All documentation is also supplied both in hard copy and as a formatted Word file for on-line viewing in color.

Usability

Metabase is a colorful, fast and fun application to use. It was designed to give you maximum control over your data in a logical and straight forward manner.

Portability

Metabase files can easily be transported on diskettes or other portable medium (or via e-mail) to be worked on anywhere.

Economical

The cost of equipping a laboratory with a custom installed Metabase system is a fraction of the cost of competing systems. The reason is because we take advantage of the power and breadth of Excel to both maximize your options and minimize your costs.

Software Link:  Metabase - pharmacokinetics/ toxicokinetics Software

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PASS - Pharmacology Software

The acronym PASS stands for Prediction of Activity Spectra for Substances. After entering structural formulas of organic compounds - either a single structure or a big library - the program instantly gives a list of predicted bioactivities, accompanied by estimated mathematical probabilities.
Details

Key features of PASS:
• Chemical structures are represented with Multilevel Neighborhood of Atoms (MNA) descriptors
• Activity spectra for libraries of compounds can be predicted within minutes
• Atoms of every structure are colored according to their contribution to the chosen activity
• Possibility to create and train own SAR bases and to modify the included SAR base
• Currently, 4,444 bioactivities can be predicted with the included SAR base
• Mathematical algorithm based on Bayesian estimates of probabilities

PASS can quickly predict biological activity spectra for organic drug-like compounds qualitatively. The activities that can be predicted range from pharmacotherapeutic effects, biochemical mechanisms and toxic and adverse effects to influence on the metabolism, gene regulation and transporter-related activities. The software runs under Windows.

PASS has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

A free demo version, as well as further information, is available upon request.

Software Link :  PASS - Pharmacology Software

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GastroPlus - Pharmacology Software

GastroPlus™ is a mechanistically based simulation software package that simulates intravenous, oral, oral cavity, ocular, intranasal and pulmonary absorption, pharmacokinetics, and pharmacodynamics in humans and animals. This smoothly integrated platform combines a user-friendly interface with powerful science to help you make faster ad more informed project decisions. GastroPlus™ is by far the most commonly used software of its kind!

The GastroPlus simulations include:

• NEW! Drug-Drug Interactions (with optional DDI Module)
• NEW! Models for predicting drug administration through ocular or pulmonary routes (with optional Additional Dosage Routes Module)
• Whole-body physiological models for human (fasted and fed), beagle dog (fasted and fed), rat (fasted and fed), mouse (fasted and fed), and cyno monkey
• Variety of dosage forms: intravenous (bolus or infusion), immediate release (tablet, capsule, suspension, solution, lingual spray, and sublingual tablet), and controlled release (gastric retention, dispersed release, integral tablet, enteric coated tablet and capsule, and buccal patch)
• Peff converter to convert user-measured permeability to human in vivo Peff
• pH-dependent solubility and logD models
• Mechanistic effect of bile salts on in vivo drug solubility and dissolution
• Enhanced treatment of nanoparticle effects on solubility and dissolution
• Dissolution and precipitation dependence on particle size, shape and particle density
• Chemical degradation of drug in intestinal lumen prior to absorption
• Enterohepatic circulation
• Parameter Sensitivity Analysis - test sensitivity of results to changes in any model parameters
• Virtual Trials - predict likely population distributions of PK/PD results
• Ability to fit one-, two-, or three-compartment conventional pharmacokinetic models to IV and/or oral data (with optional PKPlus Module)
• Physiologically based pharmacokinetics (with optional PBPKPlus Module)
• Automated model fitting for single or multiple data sets (with optional Optimization Module)
• Saturable metabolism and active transport in gut or other tissues and metabolite tracking (with optional Metabolism and Transporter Module)
• Advanced In Vitro - In Vivo Correlation for immediate or controlled release formulations (with optional IVIVCPlus Module)
• Structure-based predictions of biopharmaceutical parameters required for GastroPlus simulations (with optional ADMET Predictor Module)
• Pharmacodynamic modeling (PK/PD or PBPK/PD) with industry standard models (with optional PDPlus Module)

Software Link:  GastroPlus - Pharmacology Software

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PK Solutions - pharmacokinetic Analysis software

PK Solutions is an automated Excel-based program that does single and multiple dose pharmacokinetic data analysis of concentration-time data from biological samples (blood, serum, plasma, lymph, etc.) following intravenous or extravascular routes of administration. The program provides comprehensive tables of the most widely used and published pharmacokinetic parameters with the ease of a few mouse clicks. PK Solutions calculates results using noncompartmental (area) and compartmental (exponential terms) methods without presuming any specific compartmental model. Multiple dose and steady state parameters are automatically projected from single dose results.

The distinguishing features of PK Solutions are that it is easy, fast, and comprehensive. The program works with both concentration-time data and imported exponential terms. PK Solutions produces instant results suitable for
novice and experts, without the need for programming.

Benefits

The easiest pharmacokinetics data analysis software available.
Excel-based program provides wide flexibility in a familiar spreadsheet environment.
Provides graphs and tables of all the most widely used pharmacokinetic parameters.
Helps you analyze, record, compare, and report pharmacokinetic and ADME study results.

Features

Easy to Use

PK Solutions makes pharmacokinetic data analysis easy and fast. No programming required. Simply enter your data and with a few mouse clicks on the analysis sheet you are done. PK Solutions instantly computes and displays attractive graphs and tables of results.

Suits All Levels of Pharmacokinetic Experience

PK Solutions is used in over 40 countries by researchers, clinicians, students, and others at all skill levels who need a reliable and easy way to get pharmacokinetic data. Whether you need PK data daily or only for an occasional report, PK Solutions gives the needed results for the novice and professional user.

Comprehensive Coverage of PK Parameters

PK Solutions computes more PK parameters than any other program. More than 75 single and multiple dose pharmacokinetic results are computed from intravenous or extravascular dose data. PK parameter calculations are based on two standard methods of analysis: (1) curve-stripping (or method of residuals) to derive the exponential terms that describe the blood level curve, and (2) area under the curve calculations. PK Solutions applies both methods where applicable and compares the results side-by-side.

User Interaction with Dynamic Updates

All graphs and formulas are dynamically linked affording instant updates and immediate feedback when exploring the effect of changes in data or other inputs. For example, changing a dose interval gives an immediate redraw of the multiple dose blood level curve. Explore 'What if?' questions. Dynamic interaction helps you grasp the principles of pharmacokinetic analysis.

Record Changes - Compare Multiple Data Sets

Capture a complete listing of over 75 PK parameters for each data set. You can capture and compare the results of up to 256 data sets on a single, flexible form. A menu allows selection of parameter groups to be displayed and printed. Print reports, data tables, and graphs in color or black and white. Export or copy results and graphics for inclusion in presentations or formal reports.

Built-in Validation

PK Solutions includes the results of seven test data sets taken from the literature. Comparison of the literature values with those obtained by PK Solutions assures the scientific validity of the program. The test data can also be used to verify the reproducibility of calculations and the performance of the software. PK Solutions is used in hundreds of regulated laboratories throughout the world.

Excel-Based for Maximum Flexibility and Usefulness

PK Solutions is a Microsoft Excel program that can run on PCs using any version of Windows (Windows 3.x, 9x, NT/2000, XP) as well as on Macintosh computers. Excel provides a familiar working environment with extraordinary capabilities for additional analyses, importing and exporting of data, and interaction with other software. PK Solutions can be integrated with other Microsoft Office documents, databases, and intranet platforms. Reports and presentations of the results is easily accomplished using standard Office procedures.

Complete User Guide

The PK Solution 2.0 User Guide is a complete manual supplied in an attractive notebook. The guide clearly describes and illustrates all program options and features. In addition, the guide includes a description of all the pharmacokinetic parameters, graphing functions, and formulas used by the program thereby providing a useful compilation of pharmacokinetic equations in one place. See the PK Equations page for an excerpt from the guide describing the pharmacokinetic calculations used

Software Link:  PK Solutions - pharmacokinetic Analysis software

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ADMET Predictor - Pharmacology Software

ADMET Predictor™ is an advanced computer program that enables pharmaceutical researchers to rapidly estimate a number of ADMET properties of new chemical entities (NCE's) from their molecular structure. ADMET Predictor™ models have been consistently ranked as the most accurate in independent published comparisons.

What makes ADMET Predictor unique?

ACCURACY: its predictive models have been consistently ranked as the most accurate by independent third party comparisons.
SPEED: it can process up to ~200,000 compounds per hour on a notebook PC.
EASE OF USE: using the program is as simple as opening a file containing molecular structures.
OUTPUT OPTIONS: it provides a variety of output channels to store, transfer, or visualize its results quickly and efficiently.
BATCH CAPABILITY: it has a built-in batch mode and can run as a Pipeline Pilot™ component.
NOVEL DESCRIPTORS: it features a unique collection of rapid estimates of quantum mechanical descriptors of electronic density and reactivity at both atomic and molecular levels - a result of federally funded 3-year research project.

Software Link:  ADMET Predictor - Pharmacology Software

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ToxExpress - Toxicology Software

ToxExpress® Program is a flexible and enabling program that brings the power of toxicity-based gene expression coupled with classical toxicology endpoints to lead optimization and drug safety studies.

Toxicogenomic profiling can accelerate the pace of uncovering critical information before making significant investments into Preclinical studies. The use of microarrays to examine gene expression profiles of compounds in animal systems, when benchmarked to large reference data sets, helps establish accurate predictive methods that identify potential toxic liabilities, even in the absence of overt injury. In addition, Gene Logic's ToxExpress® Program helps to streamline, focus and augment subsequent classical studies through specialized applications that support key research areas of predictive, investigative, and mechanistic toxicology as well as safety biomarker discovery.

The products and services that comprise our ToxExpress® Program can transform and augment your critical Preclinical toxicological programs. With one service provider, you have direct access to the full spectrum of compound safety assessment technologies, providing powerful, innovative ways of resolving drug development questions and enabling targeted compound decisions.

Software Link : ToxExpress -  toxicology Software

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PKS Reporter - Pharmacology Software

Reports for internal use or regulatory submission cost pharmaceutical R&D organizations considerable staff resources to transform data, create tables and graphs, format and edit documents, validate data references and analyses, and update documents when new data are received. This work can take skilled researchers away from more productive tasks. Much of the overhead, repetition, and potential for error can be minimized by moving to an automated, standardized system to produce regulatory reports. Moreover, secure storage and version control can alleviate tedious "housekeeping" related to change tracking, document management and sign-off.

Pharsight® has developed PKS Reporter to address the need for streamlined, systematic, and automated report generation and signature. Using the Pharsight Knowledgebase Server™ (PKS™) as an underlying source of secure, regulatory-compliant report content, PKS Reporter allows researchers to use familiar tools such as WinNonlin® and Microsoft Word® to construct, update, review and approve any type of report.

PKS Reporter is directly integrated with PKS, as both a source of report content and a secure repository for report storage and version control. PKS Reporter links reports in Microsoft Word directly to PKS, where it draws report content from data and modeling results created in WinNonlin Enterprise, NONMEM®, SAS and other industry-standard modeling and analysis tools. In addition, PKS Reporter is designed to work with Pharsight's PK Automation tool and will pick up tables and graphs automatically created by WinNonlin AutoPilot. From within Microsoft Word, researchers can browse the PKS database, loading objects and values drawn from various PKS studies and analysis scenarios. When the source data change, PKS Reporter marks its content as out of date, ready for automatic update. QA staff can automate the verification of report data by simply opening the document and selecting to have all references checked. Your team can create standardize report templates specifying report layout, formatting and specific content elements. Report sign-off is smooth and automatically tracked with Reporter's signature tool and e-mail notification.

Benefits
Improve scientific productivity: standardize and automate routine document authoring tasks.
Link reports to output of WinNonlin, AutoPilot, and other industry standard software.
Reduce QA overhead: automate report updates and validation.
Ensure secure, distributed access to reports.
Trace and control report versions and signatures.

Software Link: PKS Reporter - Pharmacology Software

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