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Martin Senger [using also few slides from the presentations from the Galaxy Developers Conference 2011]

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Presentation on theme: "Martin Senger [using also few slides from the presentations from the Galaxy Developers Conference 2011]"— Presentation transcript:

1 Martin Senger [using also few slides from the presentations from the Galaxy Developers Conference 2011]

2 1. What Galaxy can do... (or could do) 2. Show me where I can try for myself 3. What can we do to make our Galaxy better...and what this is not a detailed tutorial how to use Galaxy a way to convince you that I understand everything about Galaxy

3  A web-based interface to the command-line tools (of any kind) and their combinations (“workflows”)  Galaxy performs analysis interactively through the web, on arbitrarily large datasets  Galaxy remembers what it did - history  Flexibility to include anybody’s command-line tools  by writing wrappers whose templates are available  An environment for sharing tools (or their wrappers)  “Tools Shed” repository

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6  Locally stored data  user-specific  shared between users  e.g. genome builds  Origin of data  uploaded data from your computer  using a web interface  using an FTP server  fetched from external databases (“datasources”)  only those that are “aware” of Galaxy  internally: two ways how to fetch data (async vs. sync.)  you need to be familiar with these databases and their UIs

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8 Data have metadata allowing to use data only for those tools that recognize such data types Data have attributes annotate data convert data to a new format change data type

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10  Automated set of steps – perhaps each time with different input data (of the same type)  reproducibility (usable in publications)  reusability (sharing workflows with others)  created from the scratch (using a workflow editor) or from your history

11 An example – a workflow editor Thanks to:

12 user would not have done this from the command line on our cluster

13 If we have time (6mins) click here: Creating a workflow from your history

14  Where are all these galaxies?  public servers  available immediately, free of charge   and few others, such as  usually limited resources  you cannot customize them to your special needs  KAUST/CBRC Galaxy   running on an internal cluster with limited resources  but we can do with it whatever we need to do  Galaxy in the Amazon clouds (CloudMan)  when you do not have infrastructure in house  when you have particular resource (cores, memory...) needs  when you need a customization  if you have a credit card  details in this presentation:  CloudManGalaxyOnTheCloud.pdf CloudManGalaxyOnTheCloud.pdf  Galaxy has also the RESTfull API for programmatic access (beta)

15 Image courtesy of need to:

16  Data issues  add genome-wise data we (CBRC) need  add data usable for others (Core, students...)  Tools  make a subset of tools we really need and test them fully  consider to wrap other tools (not yet available by default)  Logistics  provide user-oriented courses  create a user group to share experience and to promote knowledge  monitor its stability and usage  Hardware/sysadmin issues  Install it on better hardware (in due time)  Change the current queue priority (a chicken-egg problem)  Add an ftp server

17  Galaxy home page:   An overview presentation:  get&target=IntroductionSession.pdf


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