To check out the schedule for the bioinformatics training course, click here.

Registration is now open for the following workshops:

• • Bioinformatics Short Course
  • When: Monday, September 10, 2012 8:30am to Friday, September 14th, 2012 5:30pm
  • The course includes a rich collection of lectures and hands-on sessions. In morning sessions, leading experts in each field will introduce basic concepts as well as present real world practical examples. During the afternoons, students will have a chance to walk through software and protocols for handling next-generation data analysis. While biological and medical knowledge are helpful, students do not need to have prior programming skills to participate in the course.
• • Cloud Computing for Bioinformatics
  • When: Monday, September 17, 2012 8:30am to Tuesday, September 18th, 2012 5:30pm
  • The course is designed to get scientists up to speed quickly on the various tools and uses of cloud computing, with a focus on Amazon Web Services. Previous experience with cloud computing is not necessary, but even experienced users will find the course helpful as we focus on the latest tools and best practices for bioinformatics in the cloud.
• • Data Analysis & Visualization using R
  • When: Wednesday, September 19th, 2012 8:30am to Thursday,  September 20th, 2012 5:30pm
  • This course is designed to harness the power of the R program language and tools such as Bioconductor to make sense of the vast data coming through the next-generation sequencing technologies. We will focus on the language, statistical models, and exploration of various tools and methods of visualization.

You can also check out a summary of our Past Offerings.

We write to personally encourage you to participate in an important discussion on the topic of large data management in the cloud, with a focus on research needs. The one-day, face-to-face event is co-sponsored by Internet 2 and Microsoft, and will be held at UC Davis on Thursday, July 26th.

The curation and management of large data has become one of the largest technology challenges facing universities. While the pace of innovation of cloud services is high, a coordinated and affordable strategy to meet the needs of university researchers has yet to emerge. The discussion we plan to have at UC Davis will focus on ways we can make measurable progress in demonstrating need and innovative use of cloud technologies to manage large data for university research. The event will result in a series of pilot projects that will focus in the first phase on the area of genomics and “Bio IT” more broadly, using Microsoft’s Azure cloud computing service. UC Davis will serve as the host for this discussion, with leaders from Internet2 and Microsoft Research participating as key partners in the discussion and subsequent projects. We encourage you to attend and suggest other members of he academic community who may be interested in this discussion. (See the draft agenda for the event and background information below and attached.)
To join us, we ask that you please follow these two steps:

• Let us know if you will be participating in person or via video-conference – RSVP by replying to this message by Friday, July 20th at 12 p.m. PST
• Complete your hotel reservation, should you need one, by Friday, July 13. We have made arrangements for a group discount for two nights (07/25-07/26) under the event name of “Large Data Management Conference.” Please contact Maria at the Aggie Inn directly at (530) 753-7100, ext 113. Discounted rates range from $95-$119/night. For more information, see http://www.aggieinn.com/ .

We will work with you to establish a video conference link to your location, and will be available to answer any questions as you prepare for the event. If you would like to discuss the meeting in person, please
contact Gabe Youtsey, Assistant CIO at UC Davis, at (530) 752-0701 or gdyoutsey@ucdavis.edu .

We look forward to your participation in this event,

Sincerely,

Richard Michelmore
Professor, Molecular and Cellular Biology
And Director, UC Davis Genome Center

Peter M. Siegel
Campus CIO
And Vice Provost, Information and Educational Technology
University of California, Davis

Full Schedule

In order to ensure ample interaction among the participants, there are only 11 slots available. If you want to be considered for participation in the workshop, please have the above information to Dr. Dawei Lin by the end of business on 11/23/2010.

Day 1 classroom sessions:

• Outline phylogenomics approaches, giving selected case-histories
• Briefly review public on-line resources (SEED, STRING)

Day 1 hands-on computer sessions:

• Use STRING to recapitulate historic gene discoveries made via clustering and co-distribution
• Introduce the SEED database – its genomes, how to navigate, clustering tools, essentiality data
• Teach SEED annotation tools using selected target genes that participants annotate themselves

Day 2 hands-on computer sessions:

• Creation and curation of a SEED subsystem incorporating the above novel genes
• Using the subsystem to develop hypotheses about novel genes’ function using the subsystem

We have a few left due to people’s schedule change. This course format is designed by Dr. Andrew Hanson. The decision will be based on the need of this course and not your research program. Faculty members are encouraged to participate. For selection, we need the following information:

1. Your name
2. Lab Name
3. Your position
4. Research focus, such as Human, Animal Sciences, Plant Sciences or Microbiology
5. Will you bring a problem of your own to the course? This problem could be, for example:
   • A plant gene of unknown function that has good homologs in prokaryotes
   • An enzyme that is known to exist but for which a gene has not yet been found.
   • In case (1) we can try to predict a function for the gene; in case (2) we can try to find the gene corresponding to the enzyme.
6. Do you have the basic knowledge of the following:
   • Some familiarity with the basics of GenBank entries, Blast searches, sequence alignment and phylogenetic analysis, prediction programs for organellar targeting etc, and microarray databases
   • Elementary microbiology (e.g. that bacteria and archaea are different, that prokaryotic lifestyles and metabolic capacities differ enormously, and what operons are). Some acquaintance with KEGG pathways is helpful but few will have this.
7. DaFIS account number

The workshop will be free if completed in its entirety. However, if you cannot stay for the entire two days it will affect the course, and a participant from the wait list will be selected to fill your spot. To cover the cost of personnel effort in making these special arrangements, a $100 fee will be charged to your account.

We will have a Bioinformatics Technology Forum (BTF) presentation on “Charting unknown territories – reverse QSARs, random forests, in-silico spectra – and the hunt for the holy grail in mass spectrometry” presented by Dr. Tobias Kind, Tuesday (November 16, 2010) at 11am-12pm in room 4202, GBSF, Davis, CA.

Genetic imperialism – fact or fiction? The cost of a large GWAS (genome wide association study) can account for more expenses than the yearly funding for metabolomics by the NSF or NIH. For example the breast cancer genes BRCA1 and BRCA2 are only causative for 5% of the high risk breast cancer cases, other causes remain unknown. Yet the influences of small molecules from food sources and the environment on diseases are not well understood and need to be investigated in more detail using metabolic profiling techniques.

Mass spectrometry based metabolomics can be used to obtain a very fine-grained view at all small molecules and can be used with genomics, transcriptomics and proteomics in systems-wide approaches. The drawback is that small molecules can not be sequenced like genes and proteins, but each molecule requires on average one year and one researcher for complete structural elucidation. Many of the algorithms do not scale well on Hadoop MapReduce or cloud services, because there are actually no algorithms to deduce the correct structure from mass spectral signals.

The holy grail of mass spectrometry, the deduction of the correct structures from mass spectral information can only be found with systematic approaches and a wide range of modern cheminformatics and bioinformatics software tools. The talk focuses in more detail how reverse QSARs, random forests, genetic algorithms and in-silico spectra can be used for fishing in the sea of 10^200 possible molecules and which direction to steer on the voyage to the holy grail of mass spectrometry.

Tobias Kind is a researcher at the Metabolomics Laboratory (FiehnLab) at the UC Davis Genome Center. His interests are mass spectrometric based metabolic profiling methods and their application to fundamental disease and plant research.

The purpose of the Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at the BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. You may subscribe to the Bioinformatics mailing list for up-to-date news and follow us on twitter at @ucd_biorhythm.

We will have a Bioinformatics Technology Forum (BTF) presentation on “MapMan – a visualization tool for functional genomics” by Russell Reagan of the UC Davis Plant Sciences Dept. at 11am-12pm on 10/19/2010 (Tuesday) at Room 4202, GBSF.

MapMan is a software tool for visualization of large functional “omics” data sets, primarily transcriptome data. MapMan is especially good at displaying expression data for tens or hundreds of genes (and metabolites in some cases), together with visual representations of biological functions and pathways. The basic features of MapMan will be presented, along with its application to microarray and RNA-Seq experimental data. Examples will include crop species lacking a fully sequenced genome or direct empirical evidence for most gene functions. The challenges inherent in creating effective visual presentations for complex data sets, pathways and regulatory networks will be discussed.

The purpose of the Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at the BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. You may subscribe to the Bioinformatics mailing list for up-to-date news and follow us on twitter at @ucd_biorhythm.

There is still room available in the UC Davis Bioinformatics Core Amazon Cloud Computing Workshop being held September 21-22, 2010 in conjunction to the bioinformatics next generation sequencing data analysis workshops in the Bioinformatics Short Course. Amazon Web Services are the leading commercial cloud computing provider; and this course is ideal for people who look for additional scalable computing resource for processing large datasets.  The course will cover the most-used services in Amazon’s Cloud Computing infrastructure for bioinformatics use. Topics include everything from signup, launching cloud compute instances, loading your data in the cloud, security, public and private data sets, and more. If you’ve never used Amazon Web Services before, this course will be invaluable in getting you up to speed on the standard cloud technology in use today.

Space is limited and priority will be given on a first-come first-served basis. Sign up today by clicking on the button to the right or visiting the registration page. You may register for the Bioinformatics Short Course and the Bioinformatics Cloud Computing Workshop together, or attend them separately. If you have any questions, please contact the UC Davis Bioinformatics Core, and we’ll be happy to help, or visit the Amazon Cloud Computing page the Bioinformatics Short Course 2010 site.

The UC Davis Bioinformatics Core is pleased to provide the 2010 Bioinformatics Short Course on September 13-21, 2010. This course will cover data analysis issues appropriate for the most popular next-generation sequencing platforms, including the Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD systems.  It will provide intensive hands-on training to enhance understanding of algorithms and the limitations of different sequencing technologies.  Topics will include an introduction to the basics of sequencing technology, de novo sequence assembly, SNP discovery with or without a reference genome, ChIP-seq (Chromatin immunoprecipitation – sequencing), RNA-seq or digital gene expression, metagenomics and functional analysis using genome browsers and high performance computing techniques.

The course includes a rich collection of lectures and hands-on sessions.  In morning sessions, leading experts in each field will introduce basic concepts as well as present real world practical examples.  During the afternoons, students will have a chance to walk through software and protocols for handling next-generation data analysis.  While biological and medical knowledge are helpful, students do not need to have prior programming skills to participate in the course. On top of a week of lectures and hands-on workshops, we’re providing a 2-day course September 21-22 on Cloud Computing for Bioinformatics with emphasis on Amazon Web Services which can be purchased separately or as part of the larger course. We’ll have more information as it becomes available.

You can find more information at bsc2010.bioinformatics.ucdavis.edu, or register online at: conferences.ucdavis.edu/confreg/index.cfm?confid=495

We will have a Bioinformatics Technology Forum (BTF) presentation on “Analysis of miRNA Function in Prostate Cancer” by Dr. Cliff Tepper, Technical Director, Genomics and Expression Resource, UC Davis Cancer Center, Sacramento, CA at 11am-12pm on  6/29/2010 (Tuesday) at Room 4202, GBSF.

The mechanisms underlying prostate cancer (CaP) progression can be critically influenced by microRNAs (miRNAs). These are a class of small, noncoding RNAs that mediate post-transcriptional regulation of target mRNAs via translational repression or accelerating transcript decay as a consequence of binding to complimentary regions predominantly in the 3′-UTR. Since each miRNA can potentially target >200 transcripts and a single mRNA can have binding sites for multiple miRNAs, miRNAs and their targets constitute a complex regulatory network having widespread effects. Accordingly, it has become essential to identify the downstream targets of miRNAs in order to more accurately perform pathway modeling and predict biological consequences based upon gene and miRNA expression profiling data.  In this presentation, we’ll discuss the experimental and informatics methods that we have been utilizing in an effort to address this challenging issue.

The purpose of the Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at the BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. You may subscribe to the Bioinformatics mailing list for up-to-date news and follow us on twitter at @ucd_biorhythm.

We will have a Bioinformatics Technology Forum (BTF) presentation on “BioTorrents: A File Sharing Service For Scientific Data” by Dr. Morgan Langille at 11am-12pm on 4/20/2010 (Tuesday) at Room 4202, GBSF.

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demands for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. This presentation is on BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net and has been recently published in PLoS One ( http://dx.plos.org/10.1371/journal.pone.0010071).

Here’s a link to his BTF: BioTorrents slides available for download.

The purpose of the Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin. If you want to talk at the BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. You may subscribe to the Bioinformatics mailing list for up-to-date news and follow us on twitter at @ucd_biorhythm.