Feel free to propose your own idea. As long as it relates to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open source programmers, but make sure your proposal is also relevant.
Cytoscape 3 is now available to end-users, and we need an easy-to-use Cytoscape App which provides the following functions to support huge data sets:
To support multiple databases, you need to use TinkerPop Blueprints. The goal of this project is publish a maintainable and usable (by average biologists) App for all Cytoscape 3 users.
Language and Skills: Java, Maven, OSGi, Git/GitHub
Potential Mentors: Kei Ono, Samad Lotia
Contact: cytoscape-discuss@googlegroups.com
Beyond just the nodes and edges, it’s often helpful to annotate a network or pathway with more information, including basic graphics and text. We now have a basic annotations framework in Cytoscape 3, but there is a lot to be done. We have also proposed an API for annotations, but the existing implementation needs to be modified to conform to the API. There are also two new features that we would like to add: relative annotations (relative to a node/edge or group of nodes) and annotation groups.
Download Cytoscape 3 and play with the existing annotations capabilities. If the project still interests you contact potential mentors via the link below and we will help you refine your proposal.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
Analogy: intersecting tags can be used to narrow down search in Delicious. This could implemented in Cytoscape using parameters from CyDataTables to intelligently create the equivalent of tags. “Intelligent” refers to meaningful, recognizable attributes like GO terms, etc.
Language and Skills: Java
Potential Mentors: Scooter Morris, Alex Pico, Allan Kuchinsky
Contact: cytoscape-discuss@googlegroups.com
Similar in idea to what is provided by VistaClara with some of the advanced features in clusterMaker, e.g., dendrograms, zooming, etc.
Language and Skills: Java
Potential Mentors: Scooter Morris, Samad Lotia
Contact: cytoscape-discuss@googlegroups.com
Goal: Develop a Cytoscape plugin that allows a user to “single-click” transfer pathway data between Cytoscape and the Virtual Cell applications.
The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems providing both client- and server- based modeling and simulation capabilities. The biologically oriented Virtual Cell user interface is primarily focused on physical modeling of cellular processes, but recently incorporated support for biological pathway models compliant with the BioPAX (Biological Pathway Exchange) format and ontology. Cytoscape is an extensible, biologically oriented graph visualization and analysis tool, build using the Java OSGi framework, which provides rich support for BioPAX pathways and connectivity to pathway databases. A Cytoscape plugin (OSGi bundle) is needed which can provide “single-click” client-side transfer/update of pathway data and user selections/actions between Cytoscape and the Virtual Cell applications.
Language and Skills: Java, knowledge of OSGi is a plus
Possible Mentors: Jim Schaff
Contact: vcell-discuss
Goal: Develop a web application for querying and retrieval SBML models from Virtual Cell database
The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems using Java RMI, providing both client- and server- based modeling and simulation capabilities. The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The models and results are stored on a remote server and presently can be reviewed only in the VCell software. The development of a web application for querying VCell database would provide new resources for biologists by enabling web access to VCell database, searching and retrieving public models in VCML and SBML formats.
Language and Skills: Java, experience with Google Web Toolkit is a plus
Possible Mentors: Michael Blinov, Jim Schaff
Contact: vcell-discuss
Background: Variant data identifies genomic regions where individual base pairs are different from a reference genome. These variations (e.g., SNPs) can influence gene regulation, structure and function, and are thus associated many genetic diseases. These data sets are quick large and difficult to navigate.
Goal: To make a Cytoscape plugin that reads in variant data files and dynamically maps the data to biological networks and pathways independently loaded into Cytoscape. The plugin should provide the databases needed to perform the mapping as well as default visualization settings, such as coloring all genes with variants in coding regions red.
The plugin should:
Language and Skills: Java/Swing
Potential Mentors: Alex Pico, Paul Tang, Nathan Salomonis, Michael Heuer
Contact: cytoscape-discuss@googlegroups.com
The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems providing both client- and server- based modeling and simulation capabilities. The biological simulations run within a batch environment on a centralized computational facility, and the job submission, status and simulation results are controlled and monitored by server side capabilities. Currently, users can only check the status of long running simulation jobs and view simulation results from within the full Virtual Cell client which must be run on a laptop or desktop with sufficient resources and a standard network connection. There is a need for an iOS or android app to view job status, submit or kill jobs, manage user quotas, and provide simple results viewing.
Language and Skills: Java/Android and/or Objective-C/iOS
Possible mentors: Ion Moraru, Jim Schaff
Contact: vcell-discuss
Apply your web development skills to improve the WikiPathways website, especially the pathway page. Here are several ideas of features you could work on:
Language and Skills: JavaScript, JQuery, Web development
Possible mentors: Thomas Kelder, Alex Pico
Contact: wikipathways-discuss@googlegroups.com
OpenTutorials is a free, online tutorial resource for open source and NRNB-supported tools. It is built on top of MediaWiki and a handful of extensions. It’s basic function is to provide a wiki-based collection of tutorials that can be viewed as web page, slide show or printed handout. The wiki approach makes it easy to build and maintain content. The slide show and handout features make it useful for presenters.
There are a number of features that need to be implemented to improve the site and really make it effective to a larger community. What we’re looking for here with this project is an application that is very clear about the use cases of tutorials:
The application should include a number of features that enhance these use cases. When possible, the features should point to other examples were similar approaches have proven successful (e.g., in other popular software). After we discuss the features, your application should then include implementation details and a timeline. These would be implemented as one or more PHP extensions, for example. Experience or some demonstration of familiarity with MediaWiki or PHP would be a plus. Here are some feature ideas to get you started:
Language and Skills: PHP, MediaWiki
Potential Mentors: Alex Pico, Kristina Hanspers
Contact: apico@gladstone.ucsf.edu
Background: WikiPathways is a collaborative pathway editing and sharing platform. There are many ways to use the pathway content including data visualization and analysis. Another use is as illustrations in presentations and publications. We currently provide SVG export for this purpose. However, the images usually require quite a bit of “touch up” in secondary tools like Illustrator, which inhibits this use case.
Goal: Customize a basic SVG Editor to insert into the export process to allow basic visual style updates and custom annotations on top of the pathway image. Pre-configured options would include:
This simple “touch up” editor could dramatically increase the audience for WikiPathways to include anyone looking for an easy tool to generate nice looking pathway images for presentations. Ideally, this editor would work on tablets as well as across major browsers.
Language and Skills: SVG, SVG-edit (or alternative)
Potential Mentors: Alexander Pico, Anders Riutta
Contact: wikipathways-discuss@googlegroups.com
Goal: To develop a jQuery plugin for Cytoscape.js that allows the user to get a bird’s eye view of the graph and what part of the viewport is currently visible. The widget would behave much like the navigator control in Photoshop (image)
Motivation: This plugin would be a reusable component that could be used in many webapps that contain graph components.
Language and Skills: Javascript and jQuery required
Potential Mentors: Max Franz, Christian Lopes, Gary Bader
Contact: cytoscape-discuss@googlegroups.com
PathVisio is a pathway editor and analysis tool, which uses the GPML format to model pathways. Another standard model format is SBML, which Computational Biologists use to run simulations. An SBML importer for PathVisio would allow researchers to visualize and overlay data on the same pathway models they use in simulation experiments. Exporting these models as GPML would also allow them to be uploaded to WikiPathways for community curation.
Goals:
Language and Skills: Java, OSGi
Potential Mentors: Anwesha Dutta
Contact: wikipathways-discuss@googlegroups.com
Goal: To integrate PathVisio visualization widget into Bioclipse for visualization of pathway information from WikiPathways. Selecting protein and metabolites in the pathway visualization, will shows of that chemical entity in other Bioclipse components, using the Jmol and JChemPaint plugins for Bioclipse. Preferably, interaction can be scripted, allowing integration with other metabolomics
features in Bioclipse.
Motivation: Bioclipse is a powerful platform combining a powerful scripting language to write data analysis and visualization workflows, which can easily be shared on, for example, MyExperiment.org [1]. While it has various components to support metabolomics in general, it lacks support for visualization of metabolic pathways.
Description: You will use Java to write a plugin for Bioclipse [2] that uses PathVisio [3] as a library to visualize metabolic pathways from WikiPathways inside Bioclipse. You will use the Eclipse selection event propagation mechanism [4] so that when users select protein and metabolites, Bioclipse will automatically visualize 2D or 3D structural information about those molecules (only the event creation has to be implemented). Preferably, a scripting language extension is written [5], to allow extracting information from the pathway and highlighting of parts of the pathway. This involves extending an existing interface with methods that can be run from the scripting language.
Language and Skills: Java
Potential Mentors: Egon Willighagen
Contact: wikipathways-discuss@googlegroups.com
Goal: To integrate the new Cytoscape OSGi visualization widgets into Bioclipse for visualization of large interaction networks. Selecting protein and metabolites in the pathway visualization, will shows of that chemical entity in other Bioclipse components, using the Jmol and JChemPaint plugins for Bioclipse. Preferably, interaction can be scripted, allowing integration with other metabolomics
features in Bioclipse.
Motivation: Bioclipse is a powerful platform combining a powerful scripting language to write data analysis and visualization workflows, which can easily be shared on, for example, MyExperiment.org [1]. While it has been used in drug discovery and predictive toxicology in pharmaceutical industry [2], it currently does not have functionality to visualize large graph structures as Cytoscape has.
Description: You will use Java to write a plugin for Bioclipse [3] that uses Cytoscape. No particular graph is aimed at, but the plugin will use the Eclipse selection event propagation mechanism [4] so that when users select protein and metabolites, Bioclipse will automatically visualize 2D or 3D structural information about those molecules (only the event creation has to be implemented). Preferably, a scripting language extension is written, to allow extracting information from the
visualized graphs.
Language and Skills: Java
Potential Mentors: Egon Willighagen
Contact: cytoscape-discuss@googlegroups.com
Ensembl now provides a BioMart implementation for Ensembl genes, variation and regulation. The goal of this project is to develop a plugin that loads additional information about the data nodes in a pathway and displays them in a side panel (gene name, chromosome location, strand, %GC content, transcript count, etc). This could be extended with other services that provide other information about the data nodes.
Language and Skills: Java
Potential Mentors: Martina
Contact: wikipathways-discuss@googlegroups.com
Background: UCSF chemViz is a Cytoscape plugin that extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. The 2D diagrams can be presented as scalable independent windows or as part of a table also showing Cytoscape attributes and calculated compound descriptors, including number of hydrogen bond donors, number of hydrogen bond acceptors, molecular weight, ALogP, molecular refractivity, number of Rule of Five violations, and several more. Any of the calculated descriptors can be mapped onto Cytsocape attributes where they can be used by the VizMapper and saved with the session. More information about chemViz is available here.
Goal: While chemViz provides a number of useful capabilities, there are several deficiencies that have been pointed out by collaborators. This IDEA is to enhance chemViz by integrating a small molecule sketching tool (JChemPaint), and using the input structures to annotate nodes or to use as substructures to search within the Cytoscape network. Another enhancement would be adding support for finding small molecules in PubChem and adding new chemical descriptors that might be useful for use in drug discovery or functional analysis applications.
Language and Skills: Java
Potential Mentors: Scooter Morris, Egon Willighagen
Contact: cytoscape-discuss@googlegroups.com
Graphs can be represented in several formats, including GraphML, XGMML, SIF, and so on. The goal of this project would be to write convertors to and from formats like these and JSON.
This would allow projects on the client side (e.g. cytoscape.js) or on the server side (e.g. node.js) to read and write these graph formats.
You’ll probably want to make use of some sort of XML parsing library in JavaScript – even jQuery would probably suffice.
Language and Skills: JavaScript, XML parsing
Potential Mentors: Max Franz, Christian Lopes, Gary Bader
Contact: cytoscape-discuss@googlegroups.com
Cytoscape 3 and cytoscape.js are completely independent software packages; 3 is a Java Desktop application and .js is a JavaScript library to visualize network data. However, it shares some basic concepts, such as Visual Styles. It is very useful if we can reproduce same/similar Cytoscape 3 network views in web browsers to share/publish data sets.
The goal of this project is exporting Cytoscape 3 data as JSON, and reproducing same/similar interactive network views with cytoscape.js and other JavaScript libraries.
Language and Skills: Java, JavaScript, HTML5, Git/GitHub
Potential Mentors: Kei Ono, Christian Lopes, Max Franz, Gary Bader
Contact: cytoscape-discuss@googlegroups.com
PathVisio is a tool for pathway visualization and analysis. The pathways from WikiPathways can be downloaded and opened in PathVisio. The goal of this project is to develop a PathVisio plugin to browse, search and upload pathways in WikiPathways directly from the standalone PathVisio version. The functionality that should be supported by this plugin (can be extended):
Language and Skills: Java, OSGi, webservices
Potential Mentors: Martina Kutmon
Contact: wikipathways-discuss@googlegroups.com
BridgeDb is an identifier mapping framework used in PathVisio and WikiPathways. Currently it is possible to load a mapping databases for gene products and metabolites. The existing BridgeDb config plugin provides functionality to load more mapping databases or to use other webservices for the mappings. This functionality should be extended and integrated into the core PathVisio application as another core module. The configuration dialog has to be improved so it is more intuitive and userfriendly.
The main features of this module should be:
Language and Skills: Java, OSGi, BridgeDb
Potential Mentors: Martina Kutmon, Anwesha Dutta
Contact: wikipathways-discuss@googlegroups.com
Currently PathVisio supports publication reference annotation of pathways, data nodes and interactions with PubMed identifiers. The goal of this plugin is to provide a more advanced framework for reference annotations.
This plugin should provide (can be extended):
Language and Skills: Java, OSGi
Potential Mentors: Martina Kutmon
Contact: wikipathways-discuss@googlegroups.com
This project involves integration of support for compound nodes (hierarchically structured graphs) to cytoscape.js, a JavaScript graph library for analysis and visualization. Such support is crucial in representing biological networks (e.g. Process Description notation of SBGN [1]) The core already has support for compounds. The next step is to reflect this compound model at the core to a (default) renderer. After that a layout algorithm supporting compound structures [2] needs to be implemented in JavaScript.
[1] Refcard-PD
[2] U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, “A Layout Algorithm For Undirected Compound Graphs”, Information Sciences, 179, pp. 980-994, 2009.
Language and Skills: JavaScript
Potential Mentors: Ugur Dogrusoz, Christian Lopez
Contact: cytoscape-discuss@googlegroups.com
This project involves customizing CoSE (Compound Spring Embedder) layout algorithm [1] for biological network drawings using Process Description language of SBGN (Systems Biology Graphical Notation) [2]. A number of customizations could be implemented, including layout algorithm to consider things like substrates and products of process nodes on opposite sides and tiling of members properly inside a molecular complex. This work would improve the SBGN-ML support in paxtools [3] as well as improving the layout in the network view of cBio Cancer Genomics portal [4].
[1] U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, “A Layout Algorithm For Undirected Compound Graphs”, Information Sciences, 179, pp. 980-994, 2009.
[2] http://www.sbgn.org/Documents/Specifications
[3] http://www.biopax.org/paxtools.php
[4] http://www.cbioportal.org/
Language and Skills: Java
Potential Mentors: Ugur Dogrusoz, Arman Aksoy
Contact: cytoscape-discuss@googlegroups.com
Background: CentiScaPe is a Cytoscape plugin that allows to compute network centrality parameters. It calculates Degree, Average Shortest Path, Eccentricity, Closeness, Betweenness, Centroid, Stress and Radiality. It allows the user to analyze existing relationships between experimental data provided by the users and node centrality values computed by the plugin. Different graphic outputs and the included description of biological significance for each computed centrality facilitate the analysis by the end users not expert in graph theory, thus allowing easy node categorization and experimental prioritization.
Goal: While CentiScaPe provides a number of useful capabilities (also confirmed by more than 7000 downloads and about 60 citations in international journals), it could be significantly improved with two or more of the following additions or enhancements:
Language and Skills: Java
Potential Mentors: Giovanni Scardoni
Contact: cytoscape-discuss@googlegroups.com
This project aims to develop software, sigViz, that researchers can use to create interactive dynamic representations of cell signaling pathways that contain accurate structural details for improved communication, hypothesis generation, and systems simulation.
The sigViz app will function in a variety of popular interfaces, including web browsers, to enable researchers from any background to easily access and use the tools with no special training. A graphic user interface designed for quantitative biologists will produce outputs that target diverse audiences and purposes (e.g., journals, slides, websites, and thought/virtual experiment tools).
The GSoC sigViz project programmer will pare down, clean up, merge and build upon generalized molecular viewer and bioinformatics visualization platforms (including Cytoscape, uPy, ePMV, and Chimera) currently developed at UCSF and Gladstone to create sigViz as an intuitive cell signaling visualization and modeling app.
Visit the SigViz project site and browse all the tabs for more information about this idea!
Language and Skills: Java, Python
Potential Mentors: Graham Johnson, Megan Riel-Mehan, Scooter Morris, Alex Pico
Contact: cytoscape-discuss@googlegroups.com
WikiPathways data is now available as RDF, but to take full advantage of this representation we need better network-friendly visualization tools for RDF. Visualbox is an open source toolbox to create web-based visualizations of RDF. It currently has 12 filters ranging from tabular to Google Map projections. In this project, we would like to extend Visualbox with one or more network and pathways-specific filters.
This project could also include extending Visualbox to have better support for SPARQL query construction and validation, including but not limited to basic syntax highlighting.
Overall, the goal is to provide an RDF data viewer tailored for biologists interested in pathways and networks. Other original ideas for extensions and approaches are welcome.
Language and Skills: JavaScript, PHP, CSS (SPARQL, JS libs and tools)
Potential Mentors: Andra Waagmeister, Alvaro Graves, Anders Riutta
Contact: wikipathways-discuss@googlegroups.com
The WikiPathways motto is “Pathways for the People”. As such, we want to reach a broad audience for contributors and users of biological pathways. The next logical step is a cross-platform app for tablets.
Our existing Java Applet and JavaScript viewers and editors are being overhauled in step with updated web technologies (HTML5, JS, SVG, Canvas). This GSoC project would build on top of this work to encapsulate key browsing functionality as a table app. Some basic editing functionality might also be considered. This project would thus leverage existing technologies depending on the best starting point for translation, for example:
Ultimately, the project is about rendering our particular XML (GPML) providing search, navigation and interactivity via a tablet.
Language and Skills: Significant tablet app development experience
Potential Mentors: Andra Waagmeister,Nuno Nunes, Anders Riutta
Contact: wikipathways-discuss@googlegroups.com
Description : Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and instituions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution?
Goal: We want to build a cytoscape App that given a set of publications builds a co-publication network where node and edge types are flexible and can be selected by the users. Networks generated will help identify important nodes and edges which could be people, publications or research topics. For example, a co-publication network will have people (authors) as nodes and connections between people who have co-published together.
This functionality can be applied to several data types outside academia, whenever relationships between people is of interest. An example is professional social networks (e.g. linked-in), where individuals are connected by who they have worked with in the past or the twitter-verse where individuals are connected when they each reference the same (#) hash tag. This project will start with support for co-publication networks and extend to other networks like twitter and linked-in as time permits.
More info:
“Language and Skills” : Java, XML
Potential Mentors: Ruth Isserlin, Gary Bader
Contact:cytoscape-discuss@googlegroups.com
DynNetwork is a plugin developed during GSoC 2012 to visualize and analyze dynamic data in Cytoscape 3.0. Do you want to help us bring the application up to the next level?
We are interested in implementing the following features:
Language and Skills: Java
Potential Mentors: Jason Montojo
Contact: cytoscape-discuss@googlegroups.com
DynNetwork is a plugin developed during GSoC 2012 to visualize and analyze dynamic data in Cytoscape 3.0. Do you want to help us bring the application up to the next level?
We are interested in implementing streaming of dynamic graphs from external sources:
Language and Skills: Java
Potential Mentors: Jason Montojo
Contact: cytoscape-discuss@googlegroups.com
This project involves working on the visualization core in Cytoscape 3 (ding) to significantly improve the user experience. Currently, Cytoscape supports a single canvas to visualize the network. When moving or changing graphic objects (nodes and edges), the entire visible portion of the canvas needs to be updated. It has been pointed out by visualization experts that this problem can be easily solved by adding an additional “selection” canvas. Motion of nodes and edges could be performed in this canvas rather than the main canvas, significantly improving the interactivity on dense networks. The addition of a “selection” canvas also enables a number of visualization techniques that are too computationally expensive in the current Cytoscape model.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
Cytoscape 3 has introduce two concepts into the core, groups and annotations, that could be combined to provide a compound graph visualization. Currently groups can be either in a “collapsed” or “expanded” state. For a compound graph, a new visualization state needs to be introduced that allows the compound node (group) to be visualized as a shape (concave or convex hull) around it’s children. Moving that shape would move all of it’s children, etc.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
Cytoscape 3 includes a Network Analyzer bundle that performs a number of extremely useful network analyses. Unfortunately, the functionality provided is not exposed in a way that other plugins can utilize. This project will enhance the network analysis functionality to support calculating individual network statistics using an exported API or exported Cytoscape tasks. Moreover, the project will provide this functionality in both a GUI and non-GUI (headless) mode.
Language and Skills: Java
Potential Mentors: Scooter Morris and Nadezhda Doncheva
Contact: cytoscape-discuss@googlegroups.com
The clusterMaker plugin in Cytoscape provides a wide variety of clustering algorithms and visualizations. This project will provide significant new functionality by adding “fuzzy” clustering – that is, clustering where a node may be in multiple groups and membership becomes a probabilistic value rather than a discrete value.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
Currently, the clusterMaker plugin uses standard heat maps to visualize attribute cluster data (based on Java TreeView). Increasingly, time series data is becoming important for clustering applications and it would be useful to expand the provided visualization options to explicitly support time series data. For these purposes, we’re thinking about time-series that have multiple conditions in each series, which means we need to move beyond the standard two-dimensional heat map. This project can explore utilizing animation, small multiples, or other standard visualization techniques (or your own novel techniques) to provide new visualization opportunities to users. Ideally, this would be integrated with network-based animation tools such as DynNetwork or CyAnimator.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
CyAnimator was a key-frame style animation tool for Cytoscape 2.8. This project will implement a similar tool for Cytoscape 3, taking advantage of the existing CyAnimator where appropriate. This tool is distinct from the DynNetwork tool in that it is not necessarily driven by specific data, although one possible use case would be to create dynamic XGMML as an output from the tool.
Language and Skills: Java
Potential Mentors: Scooter Morris
Contact: cytoscape-discuss@googlegroups.com
The goal of this project is to develop a general, open source framework for performing iterative, faceted search on large data collections and networks specifically for touch-based input devices. The project will leverage ideas from existing desktop applications (see Microsoft Pivot) but will include experimentation and innovation in interaction techniques in order to create a more engaging user experience. Ultimately the framework will be applied in one of potentially many biological applications, including MedSavant, which is described below.
MedSavant is a high-performance search engine for genomic datasets, which is primarily aimed to help researchers identify genetic conditions that cause disease. The desktop client allows users to
incrementally construct faceted search queries and visualize their results virtually in realtime. Similar workflows enabled by the desktop client will be made possible by integration with the proposed
framework. For more information, visit www.medsavant.com.
Language and Skills: Android or iOS development; AJAX, JSON, Java, and Javascript; UNIX
Potential Mentors: Marc Fiume, Marta Girdea
Contact: mfiume@cs.toronto.edu
Genome wide association analysis are a commonly used tool to discover genetic susceptibility to complex traits. More than 1500 GWAS in more than 300 traits have been published to date. A common challenge in GWAS analysis is the integration of SNP signals across genes and intro biological pathways.
The Cytoscape app developed in this project would allow the following:
Language and Skills: Java
Potential Mentors: Sergio Baranzini
Contact: cytoscape-discuss@googlegroups.com
Cytoscape is often used to analyze and visualize tabular formatted experimental data in a network context, for example in clustering or finding ‘active modules’. Most often the data comes from spreadsheet of one form or another, with rows representing biological entities, such as genes, and columns representing a single column typically contains a single measurement value for one sample. Typically, the researcher has collected additional metadata about samples, for example clinical data associated with a sample, such as the age and/or gender of the patient, or smoker/non-smoker status. This kind of metadata can enable the grouping of samples into cohort sets that can be differentially analyzed and/or visualized, for example comparing cancer signaling networks for smokers vs. non-smokers. Currently Cytoscape is not set to represent metadata about samples – it is only possible via ad hoc methods and naming conventions defined by the user. The goals of this project are to (1) define and implement a systematic mechanism for representing metadata about samples in Cytoscape, (2) build interfaces and workflows for grouping samples manually and by query, comparing results of differential analyses, and (3) persisting sample set definitions across Cytoscape sessions.
See this PDF for more details.
Language and Skills: Java
Potential Mentors: Allan Kuchinsky, Zohar Yakhini, Anya Tsalenko, Mike Creech
Contact: cytoscape-discuss@googlegroups.com
During the GSoC 2012, we developed SemScape, a plugin that allows the use of Cytoscape as a browser for Semantic Web (Linked Data) knowledge bases. We are currently in the process of updating libs and packaging the plugin for the Cytoscape App Store.
The idea for this year’s project is to go one step further and to allow the use of Cytoscape to visually define queries in SPARQL. The basic idea is that from a graph, a sub-graph can be defined where a few nodes or edges can be marked as variables (and eventually filters can be associated to them): this is equivalent to a (simple) SPARQL query. The user can then define queries in a simple and interactive way, without knowing the underlying syntax, that can be stored and applied on different data sources.
The project can then be extended in three directions, depending on the interest of the student:
Some of the ideas in this project have been already prototyped, so we have a good understanding of the difficulty and timing required.
This project has the potential to make Cytoscape an ideal tool to navigate and query Linked Data resources (both in biomedical and, more generally, in Open Data domains).
Language and Skills: Java/Maven. Knowledge of OSGi would be helpful. Knowledge of Semantic Web technologies would be a plus.
Potential Mentors: Andrea Splendiani, Andra Waagmeester
Contact: cytoscape-discuss@googlegroups.com
CyThesaurus is a Cytoscape plugin providing identifier mapping services based on various resources. CyThesaurus provides utilities for mapping attributes of source ID types to new attributes of destination ID types. Currently the plugin support ID mapping resources from delimited text, PGDB file and BioMart web service. This plugin utilized BridgeDb API. CyThesaurus provides the relational database content for GenMAPP-CS, which primarily returns content and relationships derived from the Ensembl gene database.
We are now starting the port to Cytoscape 3.0 and have some interesting project ideas to make the new version even better:
Language and Skills: Java, Maven, OSGi.
Potential Mentors: Jianjiong Gao, Chao Zhang, Alexander Pico
Contact: cytoscape-discuss@googlegroups.com
