Tools available for simulations, analyses, and visualizations

Garuda Gadgets UserID:

Provide users with a single platform for implementing their varied biological analysis workflows

Garuda Gadgets Download (Windows)

Garuda Gadgets Download (Mac)

Garuda Gadgets Installation Guide

Garuda Gadgets Quick Start Manual

Garuda Gadgets Overview

Garuda Gadgets for the Review


Garuda Introduction


Garuda Data Explorer



Garuda Transcriptomics Explorer



The complexity of living systems entails the study of biology at multiple dimensions of time and space. In recent years, we have seen a explosion is large scale-omics data which aim to capture this complexity at a systems level. The availability of large experimental data sets which have high variety, variability, volume need veracity and visualisation to characterise what is commonly known as biological big data.

At the same time, in order to interpret the big data , filter the signal from the noise and lead to actionable insights, researchers need to focus on the biological small data - data which leads to meaningful information and contributes to knowledge about living systems. To extract meaningful information and knowledge from data, researchers need to use a diverse set of computational tools, algorithms, database and analytical services. Various computational approaches have been developed to study biological systems at the level of genes, transcripts, proteins, metabolites to cells, tissues organ and whole body modeling.

With the diverse and ever-increasing set of databases, novel algorithms, software and services been made available to the research community, a recurring question faced by researchers is:
How can I discover new tools for my data set and the scientific problem I wish to address?

At the same time, most analysis require the use of multiple database, tools and software in different context, and more often than not, it is not possible to define the set of tools and their sequence of connections a priori. Closely associated with discovery is the question of navigability:
How can I navigate through the different tools, services and databases in my analysis pipeline?

The complexity and multi-dimensionality of data and analytics make it extremely challenging to develop a single, stand-alone system which can integrate diverse sets of data and analysis techniques. Instead, a platform which connects the diverse components through open interfaces, and allows the community to discover and navigate through them, can provide a unique collaborative eco-system.

Garuda is an open, community-driven, common platform that provides a framework to connect, discover and navigate through different applications, databases and services in biology and medicine.

Garuda provides language independent API to connect software as gadgets, explore them through the gateway and operate them through the dashboard, all the while supported by a global alliance of leaders in computational biology and informatics.

The central driving principle of Garuda is connectivity. In this, Garuda derives its inspiration from the connectivity of the Internet, which is powered by a set of protocols (like http, tcp etc.) which together form the network stack. In order to provide a simple mechanism which allows software and services to connect in a language independent manner, Garuda works on defining a core of messages, specified in a a protocol, which can be exchanged over the standard network connection.

The driving force of the platform are the Gadgets. Any software, analytics tool or service which implements the Garuda Protocol either through the available API SDKs or its own implementation and is able to communicate with the core becomes a Garuda Gadget. The Dashboard is the personal interface for users to Garuda and gadgets, from their computers. It provides one-stop access to explore the different gadgets users have installed, check their functions and get new gadgets. The Garuda Gateway, as the name suggests, is the window to all things Garuda. Accessible via the web, it allows users to explore new gadgets available and download them to their personal dashboards.

The power of Garuda lies in the community - the Garuda Alliance. The Garuda Alliance provides an open community for researchers, developers, students from academia and industry to bring their databases, tools and services as gadgets on Garuda, connect and collaborate. In order to solve the grand challenges in bio-medicine and health, engineering an open, community-driven framework which allows diverse set of knowledge bases, data-sets, experimental systems and analytic tools to connect and collaborate is essential. An Integrated platform and not individual systems will lead the way to the future of biology.

Garuda and the SysTox Challenge

The Garuda platform will provide a one-stop shop to the Systems Toxicology Challenge by enabling users to access the challenge data, analysis and visualization tools through customized gadgets on a customized dashboard. Garuda integration will enhance the connectivity, discoverability and navigability of the SysTox Challenge.

Garuda integration will drive participant engagement through participant gadgets and leverage the Garuda Community to expand the outreach of the challenge further.

Garuda Platform will enable stake-holders of the SysTox Challenge to – Access the high quality experimental data made available by the challenge; Explore the data through customized gadgets developed by the SysTox team to visualize and analyze the data; Discover new ways to explore and analyse the data through gadgets on the Garuda Platform; Navigate through different gadgets to build novel analysis workflows.

Explore the Alliance http://www.garuda-alliance.org/

There is a short video that walks you through the Garuda experience, so if you prefer a visual approach, go straight to the video and experience Garuda In Action!
Getting started video

Learn more About Garuda here.



OpenTox Data API

API to access the data of the SysTox challenge


The sbv OpenTox API provides access to the data and metadata stored in the sbv OpenTox data warehouse developed by Douglas Connect.

OpenTox is the leading global open platform for predictive toxicology supported by open standards. The design principles of interoperability, flexibility, transparency and extensibility are key ingredients of the OpenTox Framework design and guide its architecture and implementation. It provides tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines.

Currently C57BL6-pMRTP-SW metadata and data sets are available in the sbv OpenTox data warehouse including transcriptomics, proteomics, lipidomics, lung function, histopathology scores, and additional endpoints. The API is currently used to:

  • Drive the SysTox data selection portal
  • Provide access to the SysTox data for SBI Garuda gadgets.
To search for specific datasets the API provides a combination of faceted search and full text search. Using this, the clients can query and filter the sbv OpenTox data warehouse datasets based on specific metadata facet terms and general search terms. Both search types can be used together or separately, based on the client’s needs.Specific facets currently supported by the API are:
  • Mechanism (inflammation, oxidative stress…)
  • Endpoint (molecular, histomorphometry, lung function…)
  • Tissue (cardiovascular, respiratory…)
  • Study (C57BL6-pMRTP-SW…)

It is envisioned to give access to the data API to scientists in the future. For now, all data is accessible through the Data search page.

Aperio

Online platform to visualize digitalized histopathological images

https://pmi.slidehosting.com

Login: scipi_apoe

Password: SciPiApr10


What can I use this tool for?

This online tool allows to evaluate digitalized images of tissue slides used for histopathological evaluation of the studies.



Step by step tutorial

Access to Aperio online and login

You can access the Aperio platform and view thumbnails of the slides, accompanied with group and staining annotation on any operating system and browser, and may download the high resolution images (in ImageScope sis format) to view with your own tools, if applicable.

If you want to benefit from the Webscope platform to directly view images in your browser, you must, however use either Internet Explorer (IE) or Safari with the Adobe flash player plugin.

To login on the platform to review lung and liver slides from the 8-month Apoe-/- THS2.2 study as reported in Philips et al (2016) and Lo Sasso et al (2016), please

  1. Visit the url: https://pmi.slidehosting.com
  2. Enter the Username: scipi_apoe
  3. Enter the Password: SciPiApr10
  4. Press the "User Login" button

Note that if you are inactive for a while on the platform, you will automatically be logged out and should log in again.

Access to Aperio online and login

eSlideManager - Disclaimer

  1. Press continue to skip the "research use only" warning.
eSlideManager - Disclaimer

Access to study folders

Once you have successfully logged in to the platform, you will see the list of available "projects" for review.

  1. For convenience, slides have been separated by tissue, i.e. you can access from this point either lung or liver slides from the study.
  2. To access Lung data check the box highlighted with number 2
  3. To access Liver data check the box highlighted with number 3
  4. And click "Open Data" to proceed
  5. The platform has contextual help: only the relevant section for the page viewed when accessing the "Help" are accessible
Access to study folders

Project detail page: access to the specimen

Once you have selected either the lung or the liver "project", you will view all specimen that have been assigned to that project. For the lung samples, images at 5 different levels for each animal are given for all animals per exposure group at the 2-, 3-, and 8-month time points.

  1. You can view the time point annotation and sort by this column (an up or down arrow will be displayed on the column that is currently selected for sorting the table).
  2. You can also see and sort by exposure group (sham (fresh air control), 3R4F (reference cigarette), THS2.2 (candidate RRP), cessation (fresh air exposure after 2 months of 3R4F exposure), or switch (THS2.2 exposure after 2 months of 3R4F exposure).
  3. The specimen Id corresponding to the coded animal number is given too.
  4. The date the specimen were collected is given.
  5. Note that a limited number of specimen is displayed per page, and you may find more on consecutive pages.
  6. To view slides belonging to a specimen of interest, press the + button on the left side of the row corresponding to the specimen/animal.
  7. Access to the contextual help: only the relevant section for the page viewed when accessing the "Help" are accessible
Project detail page: access to the specimen

Slides access

  1. Once you have clicked on the + button for a sample (see step#6 above), you will be able to see all slides available for a given animal. For lung, 5 different levels are given for the H&E staining and 1 level with a AB-PAS staining. For liver, 4 stainings are available for 1 level each. If you want to collapse back the list of slides, you can press the - button. Note: it is possible to expand the list of slides for multiple specimen at once.
  2. The identification number of the slide is given in the "Id" column. It is the Id that you should report having examined in the comment box of the associated questions on the SciPinion platform.
  3. A thumbnail/preview of the slide is given in the "Image" column. Clicking on the thumbnail will result in opening the image in Webscope in another tab if you are browsing with IE or Safari with the Adobe flash player or will go to a details page  or download the image window otherwise.
  4. For convenience, the Exposure group is mentioned here again
  5. Similarly, the coded animal number is given here too. Note: that may allow you to see the specific score given by the histopathologist who analyzed the study as reported in Philips et al (2016) if you download the data from the webportal (on the data search page). For more information concerning the sample preparation and evaluation method used, please refer to the corresponding section at the bottom of histopathology results in the Apoe study page on the webportal.
  6. The slide level is given in the "Level" column
  7. The type of staining is given in the "Staining" column
  8. Access to the contextual help: only the relevant section for the page viewed when accessing the "Help" are accessible
Slides access

Access to high resolution slides (zoom up to 20X)

If you have clicked on the thumbnail in the previous steps, you will see the below window in a new tab. It allows you to examine tissue slides to evaluate findings in the webscope, an online version of Leica's imagescope software.

Note: it may take a little while for the image to load, depending on your internet connection speed.

You can zoom in thanks to the zoom slider on the top left side of the window.

Access to high resolution slides (zoom up to 20X)

Metadata (ISA Format)

Format for data annotation


The metadata is provided in Investigation / Study / Assay (ISA) tab-delimited (TAB) format. ISATAB is a standardized, general purpose framework for collecting and communicating complex metadata. It consists of three files: the Investigation file (I-file), the Study file (S-file), and the Assay file (A-file). For easier manual editing, these files are combined in one excel spreadsheet. The I-file summarizes general information on the complete investigation, on all studies and all assays including people involved in the investigation, related publications and short protocol descriptions. Additionally, it relates A-files to S-files. The S-file contains information on the subject under study, its characteristics and any treatment applied. Finally, the A-file describes smallest complete units of experimentation producing data associated to a subject.


Due to the complex nature of studies like C57BL6-pMRTP-SW, the metadata is provided for each endpoint separately. Additionally, separate S- and A-files are used to describe the treatment of the animals, the data production, and the processing of the raw data. Short summaries of the proceeding steps are included in the S-tab of subsequent steps. Two columns are included e.g. in the processing S-file with information on the animal treatment and the data production for each data point, respectively. In this way, the most important metadata information for the processed data can be obtained by looking at the processing S- and A-files only.

Tableau Workbooks

Data Visualization and Exploration Tool

Tableau Workbook - Visualize study data

Tableau Workbook - Visualize study data

Packaged Tableau Workbooks are made available for large studies to allow you to more easily visualize and navigate non-omics endpoints. For omics endpoints, please refer to the tools which, as Garuda tools, are specifically meant to visualize and analyze this type of data.

You will be able to view the packaged workbook with Tableau Reader, which is a free desktop application you can use to interact with data visualizations built in Tableau Desktop. With Tableau Reader you can filter, drill down, and view data details as designed by the author.

To start interacting with the data:

  • unless you have Tableau desktop 9.2 or more recent, download Tableau Reader (free, version Tableau Reader 9.2 or more recent);
  • download the file from the study page of by following one of the links above;
  • open the Tableau packaged workbook in Tableau reader and you are ready to explore.

The tool is very intuitive, but keep reading if you need specific information...

SysTox Portal - Access from the Publication and Reports Section of the Study Page

  1. You can access the prepared Tableau workbook (when available) from the respective Study Pages, in the Publications and Reports section.
  2. Look for the tab "Tableau workbook - Visualize Data"
  3. Click on the download button to download the file on your computer.
SysTox Portal - Access from the Publication and Reports Section of the Study Page

SysTox Portal - Tableau Tools Page

  1. Quick access to the prepared Workbook packages is also available from the Tableau tools page. Click on the link of interest on the top section of page (marked (1)) to download the package workbook file on your computer.
SysTox Portal - Tableau Tools Page

Tableau Reader | Tableau Software

To be able to open the packaged Tableau workbook, you will need to either have the Tableau Desktop version 9.2 or more recent or download for free the Tableau Reader 9.2 or more recent by:

  1. Visiting www.tableau.com/products/reader.
  2. Clicking on the "download now" button and following given instructions for installation. Note. Tableau reader is available for multiple operating systems.
Tableau Reader | Tableau Software

First view - Story Page

At the start of the workbook, we have published a story (i.e., a sheet that contains a sequence of worksheets or dashboards that work together to convey information), which takes you through all endpoints available.

  1. Description of the Tableau Workbook.
  2. The navigation bar (in grey) shows all pages made available within the story page.
  3. The currently opened page is highlighted by a darker grey barckground.
  4. You can move to previous pages by clicking this left arrow.
  5. You can move to subsequent pages by clicking this right arrow.
  6. The navigation of all tabs in the workbook (where the story is one of the tabs) is always displayed on the bottom of the page. You can navigate to other tabs by simply clicking on it. The currently opened tab is higlighted by a white background while other tabs have a grey background.
  7. On the bottom right side of the view, you have buttons that allow you to move in the navigation tabs. Note: as the study is large, not all tabs can be displayed at once, and to see all available tabs, you will need to move the navigation right or left. There is also access to specific views . The view by default displays as navigation bar only the title of each tab. You cna also view thumbnails of each tab as a bottom navigation bar, or a list of thumbnails (see below).
First view - Story Page

Show filmstrip

  1. As an alternative to the tab name display only, you can also preview what is in each tab by displaying thumbnails in the navigation menu.
  2. You can then access the chosen view by clicking on its thumbnail.
Show filmstrip

Sheet sorter - All sheets quick view

  1. Clicking on the "sheet sorter" button will open this list of thumbnails view where you get a glance of all data visualizations available in the workbook.
  2. You can then access the chosen view by clicking on its thumbnail.
Sheet sorter - All sheets quick view

sbv IMPROVER tab

This tab explains on the left side what the Systems Toxicology Verification project is about and the right side recapitulates what can be done with the Tableau workbook provided.

  1. In the navigation menu on the bottom, the currently open tab is higlihgted by a white background (instead of the grey background in unopened tabs.
sbv IMPROVER tab

Study Design tab

This tab recapitulates the study design and the rationale behind the choice of some of the design parameters. It is the same than on the study page on the SysTox Portal.

Study Design tab

Test atmosphere

This is the first tab of the workbook with actual data visualization capability. The concept is the same for all other pages and will only be explained here.

  1. The name of the endpoint displayed is given here.
  2. You can select other endpoints to view by cliking on the button on the left side of the name. IMPORTANT. Boxes on the right side of the view with blue background are Filters. As the name indicate they allow you to filter/select what data you wish to display. The authors chose to display either one or multiple endpoints at once in a view. If you can select only one endpoint at a time, the button shape will be a circle as is the case here. If you are allowed to display multiple endpoints at once, a square button will be displayed instead.
  3. Boxes with yellow backgrounds are legends.
Test atmosphere

Change the view

  1. You can change the size of the figure displayed by changing the setting highlighted with (1). You have the choice to have a "normal" view optimized in width and height by Tableau, to fit the width of the page, to fit the height of the page, or to fill the full page (Entire View). Usually, the Entire View setting was selected by the authors. If you wish to see many endpoints in a figure, it may be necessary to change to Fit Width so that each endpoint displayed in a row is nicely visible.
Change the view

Highlight specific group(s)

You can have the possibility to highlight specific groups or data points. This can be done in mostly 2 ways:

  1. Click on a data point or curve
  2. Select one or multiple groups to highlight. The rest of the data will still be visible but faded.
Highlight specific group(s)

View details when mousing over data points

  1. When you mouse over a data point, information about the measurement is given.
View details when mousing over data points

Select points to focus on

  1. You can select one or multiple points by clicking and dragging your mouse over the points you want to select.
Select points to focus on

Keep only / Exclude / Mark

  1. Once you have selected points, you can right click to display a menu of choices: you can "Keep only" the points you have selected. The view will refresh to only display the points you have selected, or on the contrary "Exclude" to refresh the view without the points you have selected. You also have the possibility to add annotation of the point by cliking on "Mark Label", or draw a "Drop Line", i.e. a line between the point you selected and the axis.
Keep only / Exclude / Mark

Body weight

Average body weight per group is displayed on this graph. The presence of a "*" sign indicates that for that point, the difference to sham is statistically significant (p<0.05).

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Body weight

Biomarkers of exposure

In this tab, biomarkers of exposure can be explored. Note that you can display multiple biomarkers at once in the window if you so wish. If you display many biomarkers, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Biomarkers of exposure

Serum - Multianalyte profiling

In this tab, a panel of proteins measured in the serum can be explored. Note that you can display multiple proteins at once in the window if you so wish. If you display many proteins, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Serum - Multianalyte profiling

Hematology

In this tab, hematology results can be explored. Note that you can display multiple parameters at once in the window if you so wish. If you display many parameters, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Hematology

Plaque size - Planimetry and micro-CT results

Both results from planimetry (multiple time points) and microCT (one time point) can be visualized in this page. Note that you can display multiple biomarkers at once in the window if you so wish. If you display many biomarkers, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Plaque size - Planimetry and micro-CT results

Clinical chemistry analysis - subfractions of lipoproteins

Clinical chemistry analyses can be visualized in two different tabs. The analysis reported in this tab focuses mostly on lipoprotein fractions.

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Clinical chemistry analysis - subfractions of lipoproteins

Clinical chemistry

This is the second tab in which clinical chemistry parameters can be reviewed.

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Clinical chemistry

Histopathology (all tissues) -  Summary statistics

Histopathology data can be viewed in three different tabs, depending on the level of details. This tab displays summary statistics (mean and SEM) per exposure group and time point, for findings in the different tissues investigated. Note that you can display multiple findings at once in the window if you so wish. If you display many findings, please consider changing the view from "Entire View" to "Fit width".

Note: When you mouse-over a bar, additional statistics (min and max scores) will be displayed.

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Histopathology (all tissues) -  Summary statistics

Histopathology (all tissues) - Individual measurements

Histopathology data can be viewed in three different tabs, depending on the level of details. This tab displays single scores for a selected finding (for each level of each animal of each group), and allows to have a better grasp of the variability of scores within exposure groups and time points. Given the number of points that may overlap, it may be difficult, however, to estimate the variability within animals (especially when, for lung, 5 levels are scored).

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Histopathology (all tissues) - Individual measurements

Histopathology (all tissues) - Individual measurements - zoom in single exposure group and time point.

Histopathology data can be viewed in three different tabs, depending on the level of details. This tab displays single scores for 1 finding for only 1 exposure group  and time point. This allows to visualize variability to the smallest details.

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Histopathology (all tissues) - Individual measurements - zoom in single exposure group and time point.

Respiratory physiology (Lung function)

In this tab, parameters measured in the respiratory physiology test are displayed. Note that you can display multiple parameters at once in the window if you so wish. If you display many parameters, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Respiratory physiology (Lung function)

Respiratory physiology: pv loops

This tab focuses only on pv loops measured in the respiratory physiology tests.

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Respiratory physiology: pv loops

Bronchoalveolar Lavage Fluid (BALF) - Free lung cells counts by FACS analysis

Free lung cells measured in bronchoalveolar lavage fluid, including differentiation of cells, are displayed in this tab. Note that you can display multiple measurements at once in the window if you so wish. If you display many measurements at once, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

Bronchoalveolar Lavage Fluid (BALF) - Free lung cells counts by FACS analysis

BALF - Multianalyte profiling

In this tab, a panel of proteins measured in the bonrchoalveolar lavage fluid can be explored. Note that you can display multiple proteins at once in the window if you so wish. If you display many proteins, please consider changing the view from "Entire View" to "Fit width".

To review functionalities available when looking at data, please review the "Test atmosphere" tutorial section above.

BALF - Multianalyte profiling

AeroSolved

Computational Fluid Dynamics code for simulation of the generation, transport, evolution and deposition of multispecies aerosol mixtures.

www.aerosolved.com


What can I use this tool for?

AeroSolved is a Computational Fluid Dynamics code, based on the OpenFOAM software package, for simulation of the generation, transport, evolution and deposition of multispecies aerosol mixtures.


The AeroSolved website includes tutorial cases, documentation, and links to the code hosted in github.

AeroSolved was developed to study aerosol dynamics starting from the aerosol generation through its evolution, transport and deposition. The implemented aerosol physics is applicable to a wide range of practical applications, including the development of aerosol generators, inhalation devices, validation of aerosol delivery systems for in vivo inhalation studies and in vitro sciences as well as for atmospheric sciences. The aerosol is described within an Eulerian-Eulerian framework with the aerosol size distribution and aerosol dynamics represented by either a sectional or a two-moment method. The code is implemented on the basis of the OpenFOAM open source software, mainly taking advantage of the finite volume discretization, computation and parallelization libraries. AeroSolved was developed jointly between Philip Morris International R&D (PMI R&D) and the Department of Applied Mathematics at the University of Twente (UT), The Netherlands.

AeroSolved includes the following key capabilities:

  • Simulations of mass, momentum (Navier-Stokes equations) and energy conservation equations using a Pressure-Implicit with Splitting of Operators (PISO) algorithm.
  • Multispecies formulation for gas-vapor, liquid (droplet) phases and solid particles.
  • Aerosol physics containing the following processes:
    • Nucleation
    • Condensation/Evaporation
    • Brownian coagulation
  • Aerosol deposition:
    • Inertial impaction
    • Sedimentation
    • Diffusion

AeroSolved is publicly available following the OpenFOAM software development approach philosophy and the GNU General Public License 3.0. The software can be downloaded from a github repository (see Terms of Use for more details). You may contact us by email to learn more insights on the code capabilities or exchange of development opportunities leveraging academic and industry applications.