Tag Archives: webinar

Galaxy Intro Webinar follow-up post (July 19)

We’ll be having our July 19th Galaxy webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If have registered for the webinar, the same material will be available  in the training movie, slides, and exercises tutorial suite: http://www.openhelix.com/galaxy. You can also sign up to be informed of future webinars coming up on these topics, UCSC, ENCODE and others.

Some questions asked in today’s webinar, with answers:

1) Galaxy seems to downloadable in addition to the PSU portal and the cloud at Amazon. How would you choose?

Each has it’s purposes. From the Galaxy Wiki:
Install your own Galaxy if you want to,

a) Develop it further
b) Add new tools
c) Plug-in new datasources,
d)Run a local production server for your site because you have
Sensitive data (e.g., clinical) or
Large datasets or processing requirements that are too big to be processed on Main

Use the Cloud:

“With sporadic availability of data, individuals and labs may have a need to, over a period of time, process greatly variable amounts of data. Such variability in data volume imposes variable requirements on availability of compute resources used to process given data. Rather than having to purchase and maintain desired compute resources or having to wait a long time for data processing jobs to complete, the Galaxy Team has enabled Galaxy to be instantiated oncloud computing infrastructures”

2) Can I use Galaxy to analyze protein data?

Yes, there are a few tools for analysis on the main instance, but also you can add your own tools to a local instance.

3) What kind of local server? Can you describe the PSU instance as an example? server size, storage. filesystem , etc. ?

Check out this link for needs.

4) Can we use galaxy to align the whole genome sequences of rice to get SNPs?

This link might help.

5) Is there a link to the toolshed from the galaxy interface?

Not that I know, but this is it: http://toolshed.g2.bx.psu.edu/

6) How secure is the data we run on galaxy.psu?

 From the site (emphasis added in answer):

This is a free, public, internet accessible resource. Data transfer and data storage are not encrypted. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to any public site, including this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to setup your own local Galaxy instance or run Galaxy on the cloud.

 

UCSC Table Browser webinar follow-up post (May 24)

We’ll be having our May 24th webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If you can’t make the webinar, the same material is covered in the training movie, slides, and exercises that are freely available, sponsored by the UCSC team: http://www.openhelix.com/ucscadv. You can also sign up to be informed of future webinars coming up on these topics, Galaxy, ENCODE and others.

Free Webinars on how to use the UCSC Genome Browser

The UCSC Bioinformatics Group announces two free webinars on the UCSC Genome Browser (http://genome.ucsc.edu/). The webinars will be conducted by OpenHelix, the provider of training on 100s of free, publicly accessible bioinformatics and genomics resources.

The hour and 15 minute long webinars will cover the topics needed to effectively use this powerful, free, publicly-accessible tool. The first webinar, held Thursday, May 17 at 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT (for local time zones: http://bit.ly/ucscintrowebinar), will be an introduction to the genome browser, designed for new users of the UCSC Genome Browser, and those who want to improve their skills at basic navigation and display.

In this webinar, you’ll learn:
• to perform basic text searches
• explore and understand display feature in a genomic region of interest
• customize displays to fit your needs
• use filters to highlight data you are interested in, such as displaying non-synonymous SNPs in red to stand out
• how to set up a view the way you want, and then save that as a “Session” to share with others

The second webinar, held Thursday, May 24, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT (for local time zones: http://bit.ly/tablebrowserwebinar), will cover advanced topics including creating Custom Tracks and using the Table Browser.

In this webinar, you’ll learn to:
• perform advanced searches of the UCSC genome databases
• export and download large quantities of targeted data
• create custom tracks resulting from your advanced searches
• create custom annotation tracks of your data to share with others

Seating is limited and registration is required. Register at www.openhelix.com/cgi/webinars.cgi. Download slides before the webinar for note taking at http://www.openhelix.com/ucsc.

Seminar Summary:
What: “Introduction to the UCSC Genome Browser” and “UCSC Genome Browser: Custom Tracks and Table Browser” free webinars sponsored by UCSC Bioinformatics Group and presented by OpenHelix, LLC.

When:
Introduction: Thursday, May 17, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT
Custom Tracks and Table Browser: Thursday, May 34, 6:00 p.m. UTC/1:00 p.m. ET/10:00 a.m. PT
Who: Anyone interested in learning how to use the UCSC Genome Browser. Requires knowledge of genomic/biological concepts. No programming skills required.

Cost: No cost.

Contact Information: Register at www.openhelix.com/cgi/webinars.cgi. You will receive an email with the URL for the webinar.

About UCSC Bioinformatics Group
The UCSC Bioinformatics Group is part of the Center for Biomolecular Science and Engineering (CBSE) at the University of California, Santa Cruz. Director and HHMI investigator David Haussler leads a team of scientists, engineers and students in the study and comparative analysis of mammalian and model organism genomes. Research Scientist Jim Kent heads up the engineering team that develops and maintains the UCSC Genome Browser (http://genome.ucsc.edu), a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser — originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of mammalian and model organism genomes. The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.

About OpenHelix, LLC.
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials, web seminars, and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix also is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

OpenHelix has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found on www.openhelix.com or by calling 1-888-861-5051.

Webinars on how to use UCSC Genome and Table browsers

As we have in the past, we are offering free webinars in the coming weeks on the UCSC Genome Browser and Advanced discovery using the Table Browser and custom tracks. These have been quite popular in the past, so sign up soon!

The Intro to the Genome Browser webinar will be Thursday, May 17th at 10am Pacific time (1pm ET). Check here for your time zone.

The Table Browser and custom tracks webinar will be Thursday, May 24th at 10am Pacific time (1pm ET). Check here for your time zone.

You can register here for the UCSC Genome Browser Intro and register separately here for the Table Browser and custom tracks webinar. You’ll need to register at OpenHelix if you haven’t already. It’s free and you’ll get no emails from us unless you opt in to our most excellent newsletter  or ask to be notified of future webinars :D. Registration and attendance are free.

We have several months of free webinars planned including on ENCODE, Galaxy, PDB  and others. Keep tabs with us here or on the webinars page (or though email notification) to be notified when those free webinars are coming.

RCSB PDB Webinar follow-up post: further questions?

The February 15th “How to use the RCSB Protein Data Bank” webinar may generate some questions that we won’t have time to cover or there may be further questions that arise. So we’ll leave this blog post open for follow-up on issues that arise from our discussion. Feel free to add your questions as comments to the post.

The slides from that webinar are available here:

RCSB PDB tutorial and training materials

If you didn’t have a chance to fill out the survey, here’s the link: http://www.surveymonkey.com/s/3WZSR98

Questions from the webinar chat:

1.  We were asked about differences in what I was showing in my screenshots, and what people were seeing on RCSB PDB pages. There are two possible reasons that this might be.

The first reason is that not all structures are associated with all types of information. For example, if you compare the 2ara structure summary page to the 2arc structure summary page you will notice that the 2ara page is the apo form of the molecule and does not have a ligand, a “Ligand Chemical Component” area, or an area for External Ligand Annotation information. The 2arc structure is bound to its ligand, alpha-L-arabinose (or ARA) and so it does have both Ligand Chemical Component area and an area for External Ligand Annotation on its page. The information that you see on various RCSB PDB pages will depend on what is available for the specific entry that you are looking at.

The second reason is a bit more trivial, but equally important – RCSB PDB pages are constantly being updated, and so while the screenshots in our training materials do accurately represent the overall organization and features of resource pages, specific numbers, reference lists, etc. may change over time from what our screenshots show. We work closely with the RCSB PDB developers to keep our materials up-to-date with major software updates that would dramatically change functionality of the tools we present.

2. Another great set of questions that we got during the webinar is whether people could use our materials for their students, and where to download our free training materials on the RCSB PDB.

We would be delighted if our materials were used to teach students, or were presented as a group meeting, etc – really any non-profit use of our freely available materials is fine by us – as long as you don’t remove our copyright notices. We often “train the trainer” in our live seminars or webinars, who then go out and further the reach of our materials by using them to train others at their institutions. And we’ve heard that our materials are great to use in a classroom because not only do we offer the online modular tutorial movie that can be watched online from any browser, we also provide PowerPoint slides with the full script text, handouts for note taking, and an exercise document that can be handed out as a class assignment, or used for a classroom “walk through” discussion.

All that leads to the next part of the question, where can I download OpenHelix’s free training materials on the RCSB PDB? You can download materials free of charge, and without registering at our RCSB PDB tutorial landing page. Just click any of the buttons on the page to 1) launch the movie, 2) download any of our materials, or 3) visit the RCSB PDB resource.

 

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • Snorf. RT @szintri: “underappreciated fact of genome assembly…the choice of assemblers is often limited to those that run without crashing” via @JChrisPires [Mary]
  • RT @yokofakun: the correct URL for VARMD is http://t.co/AvNWueQU  “analyzing the DNA sequence variants produced by human exome sequencing” [Mary]
  • Found this GenomeWeb article interesting – Lot to think about/figure out: “White House Bioethics Commission Tackles Genomic Data” [Jennifer]
  • RT @drbachinsky: Personal genomes hold eventual promise for treatments – Mass High Tech Business News http://t.co/PQFqqbPf [Mary]
  • I’m working on my ScienceOnline2012 report(s), but in the meantime check out this list of blog and media coverage from before, during and after the conference here. [Jennifer]
  • Don’t forget to register & attend our free ‘How to use the RSCB Protein Data Bank’ Webinar, sponsored by the RCSB PDB. The webinar is based on our newly update, full length tutorial and will be presented next Wed. at 2 pm ET. You can register on the OpenHelix webinar page. [Jennifer]
  • RT @JChrisPires: X Prize: Build a Star Trek ‘tricorder’ and win $10m http://t.co/Vt8L63Ub via #science #technology #SciFi #Startrek #genome #bioinformatics [Mary]
  • RT @drgitlin: Will Gene Patents Derail the Next-Generation of Genetic Technologies?:  A Reassessment of the Evidence Suggests Not http://t.co/QdeiwmEp [Mary]
  • RT @m_m_campbell: A healthy marriage. Bringing human #genetics & functional #genomics together to improve #health. Great read http://t.co/AR0XZsXu @NatureNews [Mary]

RCSB PDB free webinar

I just wanted to give a heads up to our free webinar on the RCSB Protein Databank. It’s going to be next Wednesday, at 11am Pacific US time. (that’s 18:00 UTC). It’ll be about an hour, and did I say it’s free?

Seating is limited, so register early.

You can see our announcement here: http://blog.openhelix.eu/?p=11055

and you can go register right now here: http://www.openhelix.com/cgi/webinars.cgi

If you can’t make the webinar, you can check out our training materials and tutorial here (also free, sponsored by RCSB PDB)

World Tour Webinar follow-up post: further questions?

The November 10 webinar of a world tour of bioscience resources may generate some questions that we won’t have time to cover or there may be further questions that arise. So we’ll leave this blog post open for follow-up on issues that arise from our discussion.

The slides from that webinar (and movie and list of links to resources covered) are available here:

World Tour Tutorial Suite

(the “Hands on Exercises” button on the tutorial suite page is a document with a list of links of resources covered in the webinar)

-A question during the webinar was if we had a suggested sequence of tutorials to go through for bio grad (programmer). I would suggest our intro curriculum listed here (http://www.openhelix.com/cgi/curriculums.cgi)  would fulfill that need. (I’ve attached it here too: general_curriculum_v1 (downloads PDF).

 

Advanced UCSC Genome Browser Features: webinar follow-up

We will have had our second webinar on the UCSC Genome Browser on May 26th. It is an introduction to many of the advanced features and display aspects of the browser. It corresponds to the material that you can find on our UCSC-sponsored tutorial materials that are freely available here: http://www.openhelix.com/ucscadv

We will have had some time for some questions at the webinar. But there may be things we didn’t have time to discuss, or cover in enough detail. Or people may go away and try some things and then come back with further questions. This thread will serve as a place to discuss issues around the Advanced materials, the webinar, browser basics, etc. We’d also love to hear any feedback on other things you’d like to see covered in the future as well.

Some of the links used in the webinar:

UCSC Genome Browser
UCSC Tutorial (slides, movie, handouts, exercises)
UCSC Mailing Lists
Additional OpenHelix Tutorials
RepeatMasker (in answer to a question about masked repeats)
Genomics Glossary (in answer to a question about a good glossary)
LiftOver (in answer to a question about how to convert sequence between assemblies)

What did you think? Do you have questions or comments? Let us know!

Intro to UCSC Genome Browser: webinar follow-up

We will have had our first webinar on the UCSC Genome Browser on May 24th. It is an introduction to many of the basic features and display aspects of the browser. It corresponds to the material that you can find on our UCSC-sponsored tutorial materials that are freely available here: http://www.openhelix.com/ucsc

We will have had some time for some questions at the webinar. But there may be things we didn’t have time to discuss, or cover in enough detail. Or people may go away and try some things and then come back with further questions. This thread will serve as a place to discuss issues around the Introductory materials, the webinar, browser basics, etc. We’d also love to hear any feedback on other things you’d like to see covered in the future as well.

Some of the links used in the webinar:

UCSC Genome Browser
UCSC Tutorial (slides, movie, handouts, exercises)
UCSC Mailing Lists
Additional OpenHelix Tutorials
RepeatMasker (in answer to a question about masked repeats)
Genomics Glossary (in answer to a question about a good glossary)
LiftOver (in answer to a question about how to convert sequence between assemblies)

What did you think? Do you have questions or comments? Let us know!