modENCODE Blog

Antibodies against 69 C. elegans chromosomal proteins
from the Lieb modENCODE Project are now commercially available:

Below is the list of antibodies that can be purchased through SDIX’s
pre-made antibody distributor, Novus Biologicals. These rabbit polyclonal antibodies have been affinity-purified.

Alphabetical list (multiple antibodies are available for
most of these targets):

AMA-1, BAF-1, BLMP-1, CAPG-1, CAPH-2, CHD-3, COH-1, COH-3, DPL-1,
DPY-21, DPY-28, DPY-30, EFL-1, EPC-1, GAK-1, GFL-1, HCP-3, HDA-1,
HIM-17, HIM-5, HIM-8, HIS-24, HMG-3, HPL-2, JMJD-2, KLE-2, KNL-2,
LEM-2, LET-418, LEX-1, LIN-13, LIN-15B, LIN-35, LIN-37, LIN-53,
LIN-54, LIN-61, LMN-1, MES-3, MES-4, MET-1, MIS-12, MRG-1, MSH-5,
MTF-1, MYS-3, MYS-4, NASP-1, NDC-80, NPP-13, NPP-16, NPP-9, ODD-3,
RAD-51, RBA-1, REC-8, RSD-6, SCC-1, SCC-3, SDC-2, SET-2, SUN-1,
T26A5.5, TAG-192, TBP-1, TSN-1, WAPL-1, Y55F3AM.14, ZFP-1

These antibodies are being used for chromatin immunoprecipitations
(ChIP) as part of the modENCODE (Model Organism Encyclopedia of DNA
Elements) project.

A URL link for further ordering information:

http://www.sdix.com/Special-Landing-Pages/celegans.aspx

Contact information for the company:

SDIX
Strategic Diagnostics Inc.
111 Pencader Drive
Newark DE
19702-3322 USA

www.sdix.com

Tel: (302) 456-6789
Fax: (302) 456-6782
Sales: (800) 544-8881

modMine release 19

Release 19 contains 1075 submissions, 770 for D. melanogaster, 301 for C. elegans and 2 each for D. mojavensis and D. pseudoscura.

A few important additions in this release:

• Genomic Region Search: this tool allows to search for genomics features in given regions.
• The search tools is now extended to a great number of keywords and has a faceted display to simplify filtering.
• Submissions List: it is now possible to create list of submissions.
• The undelying genomic model has been updated to reflect the latest Sequence Ontology structure.

The display of GBrowse tracks related to genomic features has been improved, as the speed of the Cytoscape browser. At the same time the build process for the application has been greatly improved and is now much faster.

If  you exported CDS or mRNA features for submissions of the Waterston experiment: ‘Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions’ from the previous release of modMine (release 17) please check and re-export the data. While the CDS and mRNA features were correct for the experiment as a whole, too few were assigned to each submission.

Please contact help@modencode.org if you have any questions. Our sincere apologies for the error which is now fixed.

Lincoln Stein of the Ontario Institute for Cancer Research (OICR),
Suzanna Lewis of Lawrence Berkeley National Laboratory, and Gos
Micklem of the University of Cambridge are looking for two consultants to
work on the modENCODE (http://www.modencode.org) project, whose aim is
to discover and explore the genomes of C. elegans and D. melanogaster,
using new scientific strategies and new technologies for discovery.
Our role is to manage the Data Collection Center (DCC) for the entire
modENCODE project, and these positions will place the successful
applicant in a consortium of world-class international researchers.

This individual will be a pivotal team member, responsible for
interacting with several external research labs, as well as with
internal software developers, to collect and collate experimental data
of many different types. Several laboratories are carrying out a
diverse range of large-scale, high-throughput, novel experiments. A
background in biology will be needed to facilitate the collection of
experimental details, and perform quality control of the resulting
experimental data. This person must be able to quickly learn new
methodologies and laboratory techniques, including computational
analysis methods, and be able to understand their strengths and
limitations. In addition to a strong background in biology, the
candidate must be knowledgeable in programming and/or software
development. In such a liaison position the candidate must also
possess verbal and written communication skills, particularly for
understanding requirements from biologists, and to productively work
in a collaborative environment. The ideal candidate will have
experience with high-throughput biological techniques such as
microarrays and/or second-generation sequencing technologies (i.e.
Illumina), and analyzing the results of such experiments.

These two contracted positions for the OICR, and will be coordinated
by the team in Berkeley, CA. Ideally, you will be located in either
the Pacific Northwest (such as Seattle, WA) or East Coast (such as New
York, NY), and willing to spend an initial phase (~3-6 months) in
Berkeley, CA, and week-long visits 2x per year. Most likely you will
be situated in a home-office, and will require local travel ~25% of
the time. Contract is expected to expire at the end of April, 2011.

Required Qualifications
M.S. or higher in Biology or Bioinformatics.
Ability to use Unix/Linux command line.
Some formal training in Computer Science, such as algorithms and data
structures.
Familiarity with Perl/Ruby, and/or other programming languages
Very detail-oriented
Excellent communication skills, both written and verbal
Strong people-skills
Willing to travel locally up to 25%

Beneficial
Laboratory experience with either C. elegans or D. melanogaster
Familiarity with Object-Oriented programming, data structures, and
algorithms related to sequence analysis
Familiarity with databases and SQL
Familiarity with Wiki development
Sysadmin abilities a plus

Please contact Suzanna Lewis (suzi AT berkeleybop DOT org) with your CV and
letter of interest if this position seems right for you.