20th Annual International Conference on
Intelligent Systems for Molecular Biology

Workshops

 

Workshop 1: Navigating the granting jungle
Workshop 2: Computational Drug Repositioning and Systems Pharmacology
Workshop 3: Bioinformatics Core Facilities
Workshop 4: Workshop on Education in Bioinformatics (WEB 2012) - The Future in Bioinformatics Training
Workshop 5: P2P - From Postdoc To Principal Investigator
Workshop 6: Bioinformatics for Agriculture and Industrial Biotechnology

 
Workshop 1: Navigating the granting jungle
 
Organizers:
Yana Bromberg, Rutgers University, United States
Venkata P. Satagopam, European Molecular Biology Laboratory, Germany
 
Speaker Slides in PDF format
 
Date: Sunday, July 15     
Time: 10:45 a.m. – 12:40 p.m.
Room: 204
 
Workshop Overview: Show | Hide

Many different agencies provide funding for research activities. These exist on national levels, but also fund bi-national or international co-operation. This workshop will help current and future principle investigators from the field of bioinformatics and computational biology to get an overview of funding options and information resources available to find such funding sources. In addition, the workshop will help select those funding schemes that are promising as fitted to the individual situation (career stage, collaborators, etc).
 
While the tutorial focuses on how to write a grant application, the primary aim of the workshop will be to point researchers to the available funding options. The workshop will consist of a panel discussion and 5 invited presentations (10-20 min each with time for questions) on the following topics:
A)           Overview of funding options (individual grants, group funding, integrated projects, etc.)
B)¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†Experiences and recommendations from the writer and reviewers’ point of view
C)           How to find applicable grants and how to choose which ones to apply for
 
Programme Time Table
 
Time
Topic
Speaker
10:45-11:10
Overview of funding opportunities from EMBO, NSF, DOE – session 1
Katja Linssen, Julie Dickerson, Susan Gregurick
 
11:15-11:40
Overview of funding opportunities from EMBO, NSF, DOE – session 2
Katja Linssen, Julie Dickerson, Susan Gregurick
 
11:45-12:10
Grant writer and reviewer perspectives
Russ Altman, Stanford U
Sean Mooney, Buck Institute
12:10-12:20 BIGDATA Program at NSF Tandy Warnow, Program Director CISE/IIS - download ppt
12:10-12:40
Round Table discussion
All Participants
 
 
 
Workshop 2: Computational Drug Repositioning and Systems Pharmacology
 
Organizers:
Michael Schroeder, TU Dresden, Germany
Phil Bourne, University of California, San Diego, United States
Jacob Koehler, Dow Agro-Science, United States
 
Date: Sunday, July 15     
Time: 2:30 p.m. – 4:25 p.m.
Room: 204
 
Workshop Overview: Show | Hide
The long standing and problematic notion of designing one drug to specifically act against one target to treat one disease is slowly giving way to a more systematic systems-based approach broadly defined as systems pharmacology. In a computational sense it is where computational chemistry, bioinformatics, chemoinformatics and systems biology meet. Computational systems pharmacology is translational in that it embraces data from genotype through to electronic health records on patient cohorts. The goal of this workshop is to review the latest developments leading to new lead compounds and biomarkers, repositioning of existing approved drugs, and the use of multiple drug therapies. Together with invited leaders in the emergent field of systems pharmacology the workshop will define a course for the future, which we hope to publish as a Perspective in PLoS Computational Biology.
 

Part A. Drug interactions as markers for repurposing opportunities (2:30 p.m. - 2:55 p.m.)
Speaker: Russ B Altman, Stanford University

We have created methods for looking for drug interactions at the molecular and cellular level, as well as through logical analysis of the literature, and data mining of population-based health records. Each of these data sources individually is powerful but biased. When combined, they may yield more robust hypotheses about how drugs may combine to create unexpected response phenotypes, useful for repurposing. We have used molecular methods to propose repurposing for kinases, cellular methods for potentially repurposing parthenolide, and have found synergistic interactions between existing drugs that create responses not associated with either drug alone.


Part B. Can Computational Biology Deliver Systematic Drug Repositioning? (3:00 p.m. - 3:25 p.m.)
Speaker: Pankaj Agarwal, GlaxoSmithKline R&D

Proving that a drug that has seen human patients also works in another indication adds clear value for patients. The question for computational biology is can these predictions be made systematically with precision. We will discuss two recent methods that add to this debate. The first one uses genetics associations (from Genome Wide Association Studies – GWAS) to find new indications for drugs some of which are being validated experimentally. The second one frames the side effects of drugs as pharmacological effects, relies on the observation that many drugs that treat a disease have similar side effects, and then predicts other drugs with similar side effects as potential treatments for the disease.

Part C. Rescuing targeted compounds with combination therapy and protein interactions models (3:30 p.m. - 3:55 p.m.)
Speaker: Yves Lussier, University of Chicago

We hypothesized that unbiased protein interaction network models can unveil non-canonical mechanism of targeted therapy resistance . We identified a FDA approved drug that may sensitize resistant cancer cells by inhibiting the bioinformatically-identified aberrant molecular signals sustaining EGFR pathway activity. This network-targeting therapy, later validated in vitro/in vivo, spawned the development of our NIH Phase II clinical trial. These approaches are scalable to unveil novel interactions with canonical pathways and may apply to identifying novel targets in addition to drug rescue.

Part D. Computational Drup Repositioning and Systems Pharmacology (4:00 p.m. - 4:25 p.m.)
Speakers: Michael Schroeder, TU Dresden, Germany
Phil Bourne, University of California San Diego
Jacob Koehler, Dow AgroSciences

The long standing and problematic notion of designing one drug to specifically act against one target to treat one disease is slowly giving
way to a more systematic systems-based approach broadly defined as systems pharmacology. In a computational sense it is where computational chemistry, bioinformatics, chemoinformatics and systems biology meet. Computational systems pharmacology is translational in that it embraces data from genotype through to electronic health records on patient cohorts. Here, we briefly summarise our experiences and discuss the latest developments leading to new lead compounds and biomarkers, repositioning of existing approved drugs, the use of multiple drug therapies.
 
 
Workshop 3: Bioinformatics Core Facilities
 
Organizers:
Simon Andrews -The Babraham Institut
e
Fran Lewitter - Whitehead Institute for Biomedical Research
Brent Richter - Partners Healthcare
David Sexton - Baylor College of Medicine
 
Date: Monday, July 16       
Time: 10:45 a.m. – 12:40 p.m.
Room: 204
 
Workshop Overview: Show | Hide
 


Topic 1: Extracting biological information from diverse data sources

(Talks: 25 minutes, 5 minute break; Open Forum Discussion: 25 minutes, 5 minute break)


Scientists have typically thought of experiments in terms of using a single technology to answer a question. Technologies such as genome wide analyses have generally been performed using a single type of analysis (sequencing, microarray, mass-spec etc). However we are seeing that a complete biological picture of an experimental system can only really be gained by integrating together multiple diverse data types. Increasingly, research departments and projects are beginning to find their sequencing data limits their findings (gene associations are noisy in that the genes identified, once examined closely, usually point to other up/down stream factors) and begin to turn to data and analysis in the domains of network and systems biology. In some fields (eg epigenetics) the need for this type of integration of methylation, histone modification, nucleosome positioning, mass spec and RNA-seq is already present, but the same principle applies to most biological systems. In this session we will aim to look at the practicalities of this type of integration, including success stories, pitfalls and failures and some discussion about the tools available to help.

 

Part A: "Opportunities & Challenges with Integrating Large-Scale –‘Omics Data."
Speaker: Stephen Turner Bioinformatics Core Director, University of Virginia

This talk will show how to integrate diverse ‘Omics data to provide a fuller picture of biological function and significance of discovered variation.

Part B: "Challenges of integrating and analyzing different genomic data types"
James Cavalcoli (Director, CCDU Bioinformatics Core, University of Michigan)
This talk will focus on the tools available for data integration and how they can be used to provide the scientist with filters to narrow the data space in which they have to search.


Part C: Discussion: Extracting biological information from diverse data sources
 (11:15 a.m. - 11:40 a.m.)
To be moderated by Jim Cavalcoli, Director, CCDU Bioinformatics Core, University of Michigan and Fran Lewitter, Director of Bioinformatics and Research Computing, Whitehead Institute for Biomedical Research.

 



Topic 2: Handling the increase of demand and requirements from different sets of users within a core
(11:45 a.m. - 12:10 p.m.)

(Talks: 25 minutes, 5 minute break; Open Forum Discussion: 25 minutes, 5 minute break)

Many core facilities deal with diverse sets of users who come with very different needs. Balancing the needs of these different sets of users is a challenging task, which can be compounded by financial, regulatory or political pressures. Common headaches might include the special requirements of users working with clinical samples or for pipelines "translating" from research use to production or even clinical sequencing service. Pressure to transition and concerns of traceability, tracking, and privacy must be addressed. Additionally, external or commercial samples might come with service level agreements, which dictate the level, speed or quality of service required.

Keeping everyone happy in these situations is a potential minefield for a core, so in this session we will hear how some existing facilities have coped with these pressures, and what challenges remain. We will discuss in more detail some of the specific problems, which come with clinical applications since these present an immediate challenge affecting many of the groups.

 

Part D: Running a Bioinformatics Help Desk: from drawing colorful plasmid maps to working with HiSeq Data

Hans-Rudolf, Friedrich Miescher Institute for Biomedical Research, Switzerland
This talk will focus on the diverse population of investigators who use core services and the difficulty of satisfying all of the competing interests of those users.
 

Part E: The Challenges of Dealing with Medical Data Reinhard Schneider,  University of Luxembourg, Luxembourg
This talk will investigate the increased use of medical sequencing and the challenges this can present to an academic bioinformatics core. There are many regulatory and privacy hurdles that must be navigated by cores, which are not used to satisfying these requirements.


Part F: Discussion: Handling the increase of demand and requirements from different sets of users within a core 
(12:15 p.m. - 12:40 p.m.)

To be moderated by Brent Richter, Partners Healthcare and David Sexton, Baylor College of Medicine, Human Genome Sequencing Center.

 

Workshop 4: Workshop on Education in Bioinformatics (WEB 2012) - The Future in Bioinformatics Training
 
Organizers:
Michelle Brazas, Ontario Institute for Cancer Research, Canada
Fran Lewitter, Whitehead Institute for Biomedical Research
Vicky Schneider, EMBL-EBI
 
Date: Monday, July 16       
Time: 2:30 p.m. – 4:25 p.m.
Room: 204
 
Workshop Overview: Show | Hide


The focus of many bioinformatics training programs is on the translation of the bioinformatics tools and skills needed by their research audience. In parallel, bioinformatics training programs must also keep pace with the advances in technology that support their training efforts, such as computing in the Cloud and web-based learning platforms. There is an even greater need now to keep abreast of such technologies, since many of the newer high-throughput research methods produce such large volumes of data that trying to cover a realistic scenario of data retrieval, handling and manipulation in a classroom environment depends upon enormous computational power to store and handle such data (e.g. NGS course where read alignment involves storage and manipulation of file sizes of 1TB from a single flow cell experiment).

This workshop will consist of presentations on 1) how computing in the Cloud can alleviate the stress of insufficient computational infrastructure, make computationally intensive training programs feasible and be used to further participant skills; 2) how repositories of established, updated tutorials can promote self-directed bioinformatics training and complement onsite training programs; and 3) how the development of e-learning bioinformatics resources and the demand for self-directed learning is changing the focus of face-to-face bioinformatics training programs.

 

Part A:  Bioinformatics training in the clouds (2:30 p.m. - 2:55 p.m.)
Speaker: Francis Ouellette,  Canadian Bioinformatics Workshops, Canada
Francis Ouellette will speak on how the Cloud is being used to help run the Informatics for High-throughout Sequencing workshops offered by the Canadian Bioinformatics Workshops.

 

Part B: Bioinformatics education outside of a different box (3:00 p.m. - 3:25 p.m.)
Speaker: Trey Lathe, OpenHelix, United States

Trey Lathe will speak on how a self-directed model of bioinformatics training is pushing demand for a repository of high quality, tool specific tutorials.

 

Part C: Train online: reflections on the early days (3:30 p.m. - 3:55 p.m.)
Speaker: Cath Brooksbank, EMBL-EBI United Kingdom

Cath Brooksbank will speak on how demand for self-directed web based learning resources in bioinformatics is fueling the development of e-learning bioinformatics resources and changing the focus of face-to-face bioinformatics training programs.

 

Part D: Panel Discussion: Workshop on Education in Bioinformatics  (4:00 p.m. - 4:25 p.m.)
Speaker: Michelle Brazas, Ontario Institute for Cancer Research, Canada

Invited presentations will be followed by a panel discussion (moderated by Michelle Brazas) with the objective to project how new technologies can be incorporated into current bioinformatics training programs and how new technologies are changing the landscape of bioinformatics training.

 
Fran Lewitter, Ph.D. is the Director of Bioinformatics and Research Computing at Whitehead Institute for Biomedical Research. Her group develops materials and provides training to biologists in the Institute. In addition, Fran is a member of the ISCB board of directors and the chair of the Education committee. She is also the Education Editor for PLoS Computational Biology.
 
Michelle Brazas, PhD is the Coordinator of the Canadian Bioinformatics Workshops (bioinformatics.ca) and Manager of Bioinformatics Education at the Ontario Institute for Cancer Research. She also teaches bioinformatics in Nigeria as part of her outreach programs.
 
Vicky Schneider is the User Training Coordinator at the EMBL-EBI. She is responsible for the coordination and implementation of the EMBL-EBI’s User-Training programme (www.ebi.ac.uk/training/), which provides training for the scientific users of the EMBL-EBI’s data services.
 
 
Workshop 5: P2P - From Postdoc To Principal Investigator
 
Speakers
Gary Bader, University of Toronto
Philip E. Bourne, University of California San Diego
Florian Markowetz, Cancer Research UK
 
Organizers
Nils Gehlenborg, Harvard Medical School
Thomas Abeel, Broad Institute of MIT and Harvard
Magali Michaut, The Netherlands Cancer Institute
Venkata P. Satagopam, European Molecular Biology Laboratory
Jeroen de Ridder, Delft University of Technology
 
Date: Tuesday, July 17
Time: 10:45 a.m. – 12:40 p.m.
Room: 204
 
Workshop Overview: Show | Hide
Establishing an independent research group is an important milestone in the professional life of many scientists. This is a challenging endeavor that requires careful planning and preparation. Many questions will arise at different stages of this process: about the application, attending interviews, deciding which one is the best position to accept if one has several offers, and about negotiating the best possible deal before signing a contract. This will be followed by another phase of completely different challenges that relate to setting up a lab, such as the hiring and supervision of trainees and staff.
 
This workshop will address the most relevant of these challenges that many postdocs and newly appointed principal investigators (PI) are facing. Three experienced PIs will provide insight into the transition from trainee to PI and share advice on how to make the best out it. The workshop will be useful for scientists at all stages of the process and prepare them for this crucial phase of their career.
 

Part A: Applying (10:45 a.m. - 11:10 a.m.)
Speaker: Florian Markowetz Group Leader, Cambridge Research Institute, Cancer Research UK
 
So you have a PhD and have been a post-doc for a while or you are close to finishing up your PhD and you start wondering: “What’s next”? Do you want to stay in academia or are there any other options available? If you want to stay in academia, is it required to do a post-doc or can you move straight to the a more independent position of a PI? After careful deliberation you decide you want to work as a PI. Now what?
A number of things need to be sorted out. First of all, you need to define the position within the scientific world you want to occupy. Then you need to let your peers know what your place is and why they should care. It is important to figure out what you want to accomplish in the next 5 years and what your long-term goals are.
You are now your own ‘product’, time to start selling. First stop: prospective customers, also known as universities and institutes that may be interested in your services. Which institutes are relevant to your expertise? Do they have interesting jobs? Well, what are you waiting for?
 
Part B: Interviewing, Deciding and Negotiating (11:15 a.m. - 11:40 a.m.)
Gary Bader Associate Professor, The Donnelly Centre, University of Toronto
 
Now that you’ve landed an interview or two or ten it is time to figure out what it really means to interview for a faculty job. What is the difference between the job talk and the chalk talk? Who should you talk to and what are the crucial questions that you should ask about? Do you need to know what each and every faculty member is working on? What is it that the search committee is looking for in you? What qualities should you highlight and emphasize? Should you prepare differently for different kinds of departments (CS vs biology vs med school)?
No worries - you’ll get an offer. But not only one, you’ll get five! So it’s time for negotiations and you start wondering how you make sure that you get yourself a good start up package. What are you worth? How do you negotiate your own salary and can you get money for an administrator? What about travel funding or money to cover publication costs? And besides the money, what other criteria should you take into account before accepting an offer? Is money more important that for instance an opportunity to establish a group of local collaborators and access to excellent shared facilities? It is better to have little to no teaching commitments instead of access to outstanding students? What role should the tenure criteria play in your decision?
 
 
Session 3: Hiring and Supervising (11:45 a.m. - 12:10 p.m.)
Speaker: Philip E. Bourne Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego
 
Congratulations! You made it into a junior PI position, and you even got some money to employ one or two students. Of course, you intend to find and hire the smartest and most hard-working students in the universe to carry out your brilliant ideas. Yet, you have no experience differentiating between the suitable and unsuitable candidates. And to be honest, you do not even exactly know what ‘suitable’ means. How to determine the criteria for the perfect candidate, what are appropriate questions to ask? Do you hire someone with a lot of experience, or someone that is a fast learner?
You found someone! It was (scientific) love at first sight! There is just one catch: how to supervise this person? Surely, the new PhD student/post-doc is bright, but how to motivate him/her after a set-back or entice him/her to become more creative? It turns out to be much harder than you though to stimulate a potentially brilliant student/post-doc to actually produce brilliant work.
 
Part D: Panel discussion (12:15 p.m. - 12:40 p.m.)
All speakers
 
Of course, every experience is unique and there is no general rule. The panel discussion will give the opportunity to hear about different opinions and stories on all the topics discussed in the workshop and beyond. All speakers will be present and have ample time to discuss additional questions raised by the audience. It’s your chance to get your questions answered!
 
 
 
Workshop 6: Bioinformatics for Agriculture and Industrial Biotechnology
 
Organizers:
Chris Rawlings, Rothamsted Research, United Kingdom
Jacob Koehler, Dow Agro-science, Bioinformatics, United States
 
 
Date: Tuesday, July 17      
Time: 2:30 p.m. – 4:25 p.m.
Room: 204
 
Workshop Overview: Show | Hide


Abstract:
The aim of this workshop is to help build an ISMB community for those working on data from the genomes of species relevant to food security, energy security and industrial biotechnology. Increasing our food and energy security through sustainable agriculture and the exploitation of biotechnology are global challenges. These challenges are rising up the political and economic agenda in many countries and there are many calls for increased investment in agricultural research. The genomics revolution is only now starting to have a real impact in agricultural research and we believe that a growing and vibrant Bioinformatics community will be essential to the delivery of improved crop varieties, crop protection technologies and new biotechnological processes
Many centres (even large research organisations) working in this area have small bioinformatics groups with limited resources and we believe that an opportunity to bring people together to share experience and also to increase awareness of the interesting challenges that we face would be a good fit with the aims of ISMB meetings. Bioinformaticians working in these areas of applied science, however, face many challenges not shared by colleagues working on the usual model or medically-relevant species (e.g. yeast, human, mouse, drosophila etc). These challenges arise from fragmentation of the data landscape caused by the many boutique data resources, the incompleteness of genome information for many of the species we work on, the paucity of good reference model organisms with extensive functional genomics information and also the complexity of genome organisation in many crop species (e.g. polyploidy).

 
Part A: Harnessing Diversity – the bioinformatics challenges in Agro-ecosystems research for sustainable food production (2:30 p.m. - 2:55 p.m.)
Speakers: Chris Rawlings, Rothamsted Research, United Kingdom
 
Research and Development in agriculture depends on the cultivation, and improvement by selective breeding and genetic manipulation of plant, microbial and animal species for which the level of genomic information is severely limited by comparison with that available for the key model organisms in their respective biological kingdoms.    Furthermore, much of the information about biological function for our and other data is dispersed and fragmented in database and as web resources that have generally been developed with limited support for cross comparison and genome scale analysis. This creates problems for bioinformaticians tasked with integrating diverse datasets for interpretation and annotation of data coming from the new high throughput and high content methods for characterising gene function, phenotype and of course next generation sequencing. In addition, the application of next generation sequencing methods to studying population and ecosystem diversity (e.g. metagenomics) is broadening the range of problems that can now be tackled using molecular approaches.   The lack of reference genomes, fragmentation of functional data and huge increase in data volumes pose huge challenges for all bioinformaticians.   Some tools and resources are emerging that help us deal with these problems, but knowledge of the best approaches is not widely shared and this (probably) leads to many wheels being re-invented in groups with generally limited resources.   In this session, I will review the nature of these challenges and argue that building a more cohesive community of bioinformaticians working in agriculture and industrial biotechnology would benefit our community and ultimately the challenges of feeding and fuelling the planet by more sustainable approaches.

Part B: Analysis of Microbes, Microbial Communities, and Plants using the DOE Knowledgebase (3:00 p.m. - 3:25 p.m.)
Christopher Henry , Argonne National Laboratory, USA
 
The Systems Biology Knowledgebase (KBase) has two central goals. The scientific goal is to produce predictive models, reference datasets and analytical tools and demonstrate their utility in biological research relating to bioenergy, carbon cycle, and the study of subsurface microbial communities. The operational goal is to create the integrated software and hardware infrastructure needed to support the creation, maintenance and use of predictive models and methods in the study of microbes, microbial communities and plants. The microbial component of the KBase will be centered around an analysis pipeline that will include annotation of genome sequences, reconstruction of metabolic pathways and regulons, generation of metabolic and regulatory models, and reconciliation of models with existing ‘omics datasets and new datasets uploaded by a user. KBase will provide access to this database and analysis pipeline via a powerful programmatic interface and an intuitive socially-enabled web interface. The plant component of the KBase will allow¬† users to model genotype-to-phenotype relationships using metabolic and functional networks as well as phenotype measurements and various omics data. Plant Kbase will also support the reconstruction of new metabolic and functional networks. To accomplish this goal, KBase will provide interactive, data-driven analysis and exploration across multiple experiments and diverse
 
 
Part C: Integrating and Interpreting Genomic Data: An “exploding” challenge for model and non-model organisms (3:30 p.m. - 3:55 p.m.)
Speaker: Timothy Swaller, Director of Information Technology and Genomics, Ceres, Inc. , United States
 
The rapid explosion of both internally and externally developed experimental data of model and non-model organisms alike is causing a bottleneck on how best to use and integrate this data with already available public and private information resources. The size and complexity of these genomes in combination with the uptake of next-generation sequencing technologies is causing a significant challenge in the management, translation and use of this data. In addition, there continues to be an increase in innovative analytics which further complicates interpretation of results. These current and growing obstacles cause researchers to struggle with the best way to utilize these new information resources. Researchers and institutions routinely need to decide whether to allocate resources to the analysis of externally or internally developed data to ensure the best datasets are available for research efforts. Due to interpretation challenges with external data, internal data is routinely prioritized leading to a growing set of external data and results that never fully realize its potential. This scenario can be much improved if researchers could easily pull together different datasets and obtain integrated views that combine internal and external data. To this end, Ceres has developed software which allows integration of large, complex genomic datasets and results. The software allows researchers to visualize, compare and explore through experiments and data in a dynamic and responsive fashion. Information is used and maintained, no longer cast aside to focus on the next new experiment. This allows researchers to efficiently use their time and also to effectively consume data by continually building upon established datasets, producing better integrated and validated decisions.
 
Part D: The role of Bioinformatics in applied Agriculture and Industrial Biotechnology (4:00 p.m. - 4:25 p.m.)
Speaker: Jacob Koehler, Global Leader Bioinformatics, Dow Agrosciences, USA
 
Biotechnology has a broad range of Industrial applications. The majority of public and commercial Bioinformatics resources are human centric, i.e. they are primarily applicable to Pharma and Medicine related applications. In this session, we will review non-human Biotech applications, such as agriculture and food production, bio-processing, fermentation, bioremediation and waste treatment. These applications cannot be addressed by specializing on a small number of model organisms. For Bioinformaticians working in these areas, the majority of the public and commercial resources are of limited use. In spite of the diversity of these approaches, there are commonalities between these different Biotech applications. We will discuss these commonalities in order to identify common Bioinformatics tasks and activities. This will lead to the discussion of tools and resources that can be leveraged across the different applications. Further, we will also discuss the importance of a diverse range of unique resources and methods, that are highly specialized towards specific applications.


 

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