Nabble - Bio.net - Bio-www

Reactome Pathway Database User Survey

2009-10-04T20:40:50Z

Reactome is a curated database of core pathways and reactions in human
biology. Information is authored by expert biological researchers,
maintained by the Reactome editorial staff and cross-referenced to
several third-party databases. Reactome has an entity-level pathway
viewer and data mining tools to facilitate searching and visualizing
pathway data and the analysis of user-supplied data sets. Furthermore,
Reactome has increased its utility to the model organism communities
with improved orthology prediction methods allowing pathway inference
for 22 species. Reactome's data content and software can all be freely
used and redistributed under open source terms.

Reactome is committed to providing access to high-quality pathway
information and helpful data analysis tools. With this in mind, we
are actively soliciting comments from the research community in order
to assess community needs. We are interested to hear about your
experience with Reactome, and would like to know a bit about your
background and research interests so that we can continue to improve
the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Thank you for taking part.

Robin Haw
Manager of Reactome Outreach
Outreach [at] reactome.org
http://www.reactome.org

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Distance courses for biologists

2009-09-16T08:23:52Z

At the University of Manchester, UK, we have over 10 years experience in
running a range of online courses in computational biology. These
courses are designed to enable biologists and computer scientists to
update their skills while remaining in the workplace. They are also
very suitable for home study, helping you to keep in touch with a
research environment while taking a career break.

The courses beginning on 5 October 2009 include:

Introduction to Bioinformatics
Bioinformatics for Systems Biology

'Introduction for Bioinformatics' covers the methods and resources for
sequence data. It would be a useful course for people interested in
areas such as metagenomics or multi-locus sequence typing.

We are also have funding from the BBSRC (http://www.bbsrc.ac.uk/) to
develop new courses in computational systems biology. The first of
these courses, Bioinformatics for Systems Biology, is running in
October. It will be followed by :

Mathematics for metabolic modelling and
Computational simulation and analysis of biochemical networks

You will find further information, including fees and a link to the
online application form, here:
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the suitability of the courses for your own
professional development, please contact Heather.Vincent@...

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EMBL Events - Please subscribe

2009-06-23T07:20:21Z

Dear Colleagues,

we would like to invite you to join our mailing list to receive information about events taking place at the European Molecular Biology Laboratory.

Please use the following link to subscribe to our mailing list to receive our newsletter, event posters or e-announcements:

http://www.embl.de/events/newsletter

If you do not wish to receive any information from EMBL, please reply with the subject "unsubscribe".

Thanks for your interest in our events.

Best wishes,

the Team of the EMBL Course & Conference Office

.........................................................................................................
European Molecular Biology Laboratory
Course & Conference Office
Meyerhofstr. 2
69117 Heidelberg
Germany

Email: conferences@...
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Electronic Laboratory Notebooks (ELNs)

2009-06-17T06:50:55Z

It's clearly time to make the change to the paperless lab. In tough
economic times, research organizations all over the word are placing
increasing emphasis on legal accountability, commercial patent
protection, secure collaboration and intellectual property rights.
Subsequently, many researchers are finding that taking notes with
pencil and paper, and storing digital information in ad-hoc,
unstandardized or non-compliant systems can be legally risky,
expensive and inefficient. More and more organizations are seeing the
benefits of storing and managing their research assets in a
centralized server-client system that allows workgroup organization,
controlled access, advanced searching and authenticated audit trails.
Finally, administrators can instantly see WHO is performing research,
WHEN and WHY they did it, and exactly WHAT was discovered and recorded.

CERF by Rescentris is a cross-platform, fully compliant, state-of-the-
art, award-winning lab notebook and document management software
solution (also known as an Electronic Lab Notebook or ELN). CERF can
help organizations of any size gather, track and manage research data.
CERF is also highly customizable and extensible, capable of
interfacing with other sources of data in ways that administrators can
closely control.

Rescentris is based in Columbus, Ohio. We were founded by and are
mainly staffed by former research scientists. We will not be undersold
by any comparable server-client software solution. In some cases we
can offer free trials to customers who aren't quite sure how our
laboratory notebook software can help them.

If you know of any research groups that are about to embark on an
expensive new research project, a risky collaborative venture, or
research in a strictly regulated or legally "high stake" sector, I
would strongly urge you to tell them to investigate the use of ELN
software as a way to protect their R&D investment and avoid
accountability issues that can be the result of poor research record-
keeping.

You can lean more about our company at www.rescentris.com.

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Toy company about Evolution for Kids

2009-06-03T12:17:15Z

Forgive the intrusion, but I am writing to let the scientific and
educational communities know about a new toy company dedicated to
teaching younger kids about evolution, www.charliesplayhouse.com
("Games and Toys Inspired by Darwin"). The first toy is an 18-foot
long timeline that introduces kids to over 60 amazing creatures that
have sprouted up in the last 600 million years.

The company was founded because there are literally no toys out there
focusing on evolution even though the market is replete with toys
about chemistry, physics, astronomy, and virtually any other branch of
science. The big toy companies also shy away from the subject because
of fears of a political backlash from creationists.

Please help me spread the word about this company. It's not easy to be
starting a company right now, but it's especially hard when so many
educators and parents think evolution is a subject little kids can't
handle. Of course, it is, and this company even makes it fun.

www.charliesplayhouse.com

_________________________
Lawrence Goodman
w- (401) 626-4704
goodman.lawrence@...

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BPROM question

2009-02-03T07:30:09Z

Dear Victor (or whomever may be at the other end of this email...),
Thanks for the great software at softberry :)
I have been exploring BPROM to predict promoters 150 bp upstream of
various predicted ORFs, but I have a question I still cannot resolve.
Can you give me any advice, or where to look, to determine an acceptable
linear discriminant function threshold by which I should consider the
predicted promoters true positives? Is there an accepted norm for BPROM
or the application of linear discrimination here?

Thanks very much for your help!

Cheers,
Melissa Duhaime

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Fwd: Protein diameter

2009-01-27T01:17:33Z

BIOSCI blacklist (yw-out-1718.google.com ) ?

---------- Forwarded message ----------
From: Dan Bolser <dan.bolser@...>
Date: 2009/1/27
Subject: Re: [Bio-www] Protein diameter
To: Benjamin Walter <benwalter44@...>
Cc: bio-www@...

Interesting question.

you could look at the bounding box which is a diameter by some
definition. However, most people use the radius of gyration, which is
actually a measure of how compact the protein is.

There have been lots of studies on protein density.

HTH,
Dan.

2009/1/26 Benjamin Walter <benwalter44@...>:

> Dear friends
>
> I would like to ask whether there is some way to measure the diameter of a
> molecule (its longest diameter). (On protein database or the like web
> site).
> One way (on Jmol viewer) is to measure a distance between two extremeties of
> a given protein.
> However, this method is subject to chance of missing the longest diameter.
> Could you please help?
>
> Best regards,
> Ben
> _______________________________________________
> Bio-www mailing list
> Bio-www@...
> http://www.bio.net/biomail/listinfo/bio-www
>

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Protein diameter

2009-01-26T13:56:43Z

Dear friends

I would like to ask whether there is some way to measure the diameter of a
molecule (its longest diameter). (On protein database or the like web
site).
One way (on Jmol viewer) is to measure a distance between two extremeties of
a given protein.
However, this method is subject to chance of missing the longest diameter.
Could you please help?

Best regards,
Ben
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Hair Today, Gone Tomorrow: Tracking Hair Loss And Growth Mathematically

2008-12-11T21:42:42Z

CSIRO’s Biotech Imaging team, who specialise in developing software to
analyse images automatically, worked with a UK personal care products
company to find a way to objectively test how well their hair removal
products work.
Hair counting is often done manually by human assessors. “It’s a
boring job and results are prone to errors and variations between
different people,” Dr Pascal Valloton, Leader of Biotech Imaging at
CSIRO said.

“Our software uses images captured by a small flatbed scanner pressed
onto the skin. The software crunches the numbers to analyse the image
of skin and hairs.

“Then, almost instantly, it reports information about the length and
number of hairs in the picture.

“You can compare the results with earlier images to see if hair is
growing quickly or slowly or has been properly removed by, say, a
depilatory cream.”

Tonny
--------------
Portal to share biological information-data between people
http://biospace.ethz.ch

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RSG-India at HGM - Notice

2008-09-17T21:36:13Z

RSG-India at HGM 2008!

We are very happy to inform you all that RSG-India has been given an
opportunity to have a booth at the Human Genome Meeting 2008 to be
held at Hyderabad from 27th-31st September 2008!

Regional Student Group – India (RSG-India) is a student organization
dedicated to the development of the Bioinformatics and Computational
Biology student community in India. RSG-India is part of an initiative
by the Student Council of the International Society of Computational
Biology [ISCB-SC] to improve Computational Life sciences’ research and
learning around the world at a closer and more involved level.

HGM is the annual conference organized by the Human Genome
Organization HUGO, designed to update and increase knowledge in the
field of Human Genome research. HGM is one of the ‘must-attend’
conferences in the international conference calendar. We at RSG-India
are very excited about this opportunity. As far as we know, this is
the first time a student organization has been allowed its own booth
at an international Conference of this stature.

If you are a student interested in Computational Biology or
Bioinformatics, and will be attending HGM 2008, we would really like
to meet you and discuss any ideas that you might have regarding the
future development of Bioinformatics and Computational Biology in
India. Please do drop in at the RSG-India booth at HGM 2008.

For further details about RSG-India please visit our website
www.iscbsc.org/rsg/rsg-india or the RSG-India message board
http://groups.google.co.in/group/rsg-india. If you have any questions
regarding this, or would like to contact us, please do drop in an e-
mail at rsg-india@....

Best regards,
Team RSG-India

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CAIcal: web server to assess codon usage adaptation

2008-09-16T09:11:37Z

CAIcal is a web server that performs several computations in relation to
codon usage and the codon adaptation of DNA or RNA sequences to host
organisms.

This web server is freely accessible at http://genomes.urv.cat/CAIcal

For more details see the article Puigbo P, Bravo IG and Garcia-Vallve S.
(2008) CAIcal: a combined set of tools to assess codon usage adaptation.
Biology Direct, 3:38.
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regarding perl source code

2008-09-12T20:38:08Z

dear sir,
I am working as senior lecturer at sastra university,
tanjore. I am interested in bioinformatics. If you send me
the perl code for multiple sequence alignment. It would be
great help for my academeic endeavour.
with regards
m.a.k Jailani
senior lecturer
sastra university
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electrostatic grid modelling using VMD

2008-08-21T12:16:55Z

Dear all,

I am a beginner for VMD software, and currently try to practice VMD to get
electrostatic grid of protein of my interest. I try to use the example of
potsel.tcl usage in (http://www.ks.uiuc.edu/Research/vmd/script_library/)

source potsel.tcl
mol pdbload 1bnf
set sel [atomselect top "not water"]
potSel $sel 63 2 80

But, it did not work out, and written

couldn't execute "touch": no such file or directory

Do you know how I can get the "touch" file?
If you have more examples for me, I will really appreciate it.

Thanks a lot in advance.

Best regards,
Yusdy

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Analysis of Next Generation Sequencing data

2008-07-29T06:17:22Z

Dear Group members,

a recent Science publication:
"A Global View of Gene Activity and Alternative Splicing by Deep
Sequencing of the Human Transcriptome"
[url]http://www.sciencemag.org/cgi/content/abstract/1160342[/url]

demonstrates capabilities of two products from Genomatix
[url]www.genomatix.de[/url]

Genomatix delivers powerful turnkey solutions downstream of Next
Generation Sequencing (NGS) devices, following the Genomatix tradition
of highest scientific standards and cutting edge technology.

Genomatix solutions work with data from all available NGS system
providers: Illumina´s Genome Analyzer (Solexa), Roche (454), The SOLiD
TM System by Applied Biosystems, and HeliScope by Helicos.

Genomatix Mapping Station (GMS) delivers ultra-fast mapping of
sequence reads of any length above 9 base pairs. Ten million typical
NGS reads of variable lengths are perfectly and uniquely mapped to the
human genome in less than 30 minutes. GMS is flexible and allows for
any number of indels and point mutations, delivering an uniqueness
measure for each mapped read. It takes the NGS system internal error
checking into account and detects new SNPs. Cutting edge technology
identifies splice junction tags for advanced transcriptome analysis.

Genomatix Genome Analyzer (GGA) is the complete solution for ChIP-seq
and transcriptome analysis downstream of mapping the NGS system reads
to the genome with the Genomatix Mapping Station, or any other
technology. Terabytes of annotation data complement the results from
the NGS experiment and expand by optional integration with each new
sequencing run to a customized genome database. Easy-to-use
visualization and genome wide correlations allow for meta-analysis of
all kind of data-sets.

Integrated comparative genomics procedures allow for phylogenetical
conservation analysis of findings.

Genome wide transcription factor analysis, gene regulatory region
analysis, regulatory SNPs, epigenetic modification analysis, DNase-
seq, digital gene expression with normalization and quantification of
expression values… all required data and hardware in one technology
unit at your lab. GGA is operated through a comprehensive easy-to-use
web based interface for the biologist, plus features full data
structure access and command line driven procedures for the bio-
informatician for easy integration into own high-throughput pipelines.

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Grid/Nano

2008-07-21T10:47:29Z

Dear All
Due to I am working on a project I need some information.
Any of you are working on Grid computing And/Or Nanomedicine Or
Nanoinformatics?
Thanks!

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Errors in protein structures

2008-04-08T06:12:18Z

Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

The NQ-Flipper Team
CAME - Center of Applied Molecular Engineering
University of Salzburg
Austria

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[Protein-analysis] Errors in protein structures

2008-04-08T06:12:18Z

Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

The NQ-Flipper Team
CAME - Center of Applied Molecular Engineering
University of Salzburg
Austria

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Automated Biorepositories: Successful Models

2008-02-14T23:10:30Z

Meeting Announcement
Automated Biorepositories: Successful Models

Dear colleagues,

LRIG will host a second annual meeting on biorepositories with an emphasis
on how automation has been successfully applied to solve problems with
managing collections. The meeting consists of a technology exhibition, tours
of RUCDR and social period followed by presentations and discussion. It will
take place at Rutgers, the State University of New Jersey in Piscataway, NJ
from 3:00-9:00 PM on February 28, 2008. The web page with full details may
be found at <http://lab-robotics.org/Mid_Atlantic/meetings/0802.htm>.

An abbreviated agenda:

Tours: Rutgers University Cell and DNA Repository (RUCDR)
Dr. David Toke, Associate Managing Director, Rutgers University Cell & DNA
Repository (RUCDR)
>From 3:00 PM to 6:00 PM, Dr. Toke will conduct tours of the Rutgers
University Cell and DNA Repository.

Presentation: Development and validation of the UK Biobank sample handling,
processing and archiving protocol
Tim Peakman, Executive Director, UK Biobank

Presentation: Implementation of the UK Biobank
Paul Downey, Director of Operations, UK Biobank

Presentation: The Pfizer Liquid Store, DNA & BioFluids REMP Store
Craig Hines, Manager, Liquid Store Center of Emphasis, Pfizer - Kings
Heights Technology Center
Diane Johnson, Head of DNA & BioFluids Center of Emphasis, Pfizer - Kings
Heights Technology Center
Leonid Vodonos, Facility Manager, Pfizer - Kings Heights Technology Center

Presentation: The Rutgers University Cell and DNA Repository
Dr. Andrew Brooks, Associate Director of Technology Development for the
Rutgers University Cell and DNA Repository (RUCDR)

Presentation: ISBER
ISBER is the leading international forum that addresses the technical,
legal, ethical, and managerial issues relevant to repositories of biological
and environmental specimens.

Exhibitors include: Applied Biosystems, ArcticWhite, BioMicroLab, Brady
Corporation, C&R Laboratory Equipment, Cosmo Bio, Genvault, Hamilton Storage
Technologies, Hudson Robotics, ISC BioExpress / Micronic, Laboratory
Disposable Products, LabVantage Solutions, Phenix Research Products, Qiagen,
REMP, Tecan Group, RTS Life Science, The Automation Partnership, Thermo
Fisher Scientific / Matrix Liquid Handling Solutions, Tomtec, Worldwide
Glass Resources .

We have a complimentary menu, courtesy of the exhibitors, consisting of deli
buffet and hot entrees beginning at 3:00 PM.

The Laboratory Robotics Interest Group (LRIG) is a continuously growing
special interest group focused on laboratory automation. Our membership
consists of over 9,000 scientists and engineers. We are a non-profit group.
No dues are collected, and no fees are charged to attend meetings.

We hope to see you there!

Thank you,

Andy Zaayenga
Executive Chair
The Laboratory Robotics Interest Group
web site: http://lab-robotics.org

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E-CAI: web server to estimate an expected value of CodonAdaptation Index (eCAI)

2008-01-30T13:58:35Z

The E-CAI server is a web-application and an
executable program that calculates the expected value of the Codon Adaptation
Index (CAI) for a set of query sequences by generating random sequences with
similar G+C content and amino acid composition to the input. This expected CAI
therefore provides a direct threshold value for discerning whether the
differences in the CAI value are statistically significant and arise from the
codon preferences or whether they are merely artifacts that arise from internal
biases in the G+C composition and/or amino acid composition of the query
sequences.

E-CAI is freely accessible at
http://genomes.urv.cat/CAIcal/E-CAI

For more details see the article Puigbo P,
Bravo IG and Garcia-Vallvé S. E-CAI: a novel server to estimate an expected
value of Codon Adaptation Index (eCAI). BMC Bioinformatics 2008, 9:65

--------------------------------------------------------------------------------------------------------------------
Dr. Pere Puigbò Avalos, PhD
Evolutionary Genomics Group,
Biochemistry and Biotechnology Department,
Rovira i Virgily University.
C/Marcel·lí domingo s/n. 43007. Campus Sescelades. Tarragona.

Phone: 0034.977.55.84.86
Web Page: http://genomes.urv.cat
E-mail: ppuigbo@...
--------------------------------------------------------------------------------------------------------------------
Visit:
* HEG-DB at http://genomes.urv.cat/HEG-DB
* OPTIMIZER at http://genomes.urv.cat/OPTIMIZER
* TOPD/FMTS at http://genomes.urv.cat/topd
--------------------------------------------------------------------------------------------------------------------
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New Google custom search engine for Bioinformatics journals:

2007-07-23T14:12:09Z

Dear all,

We are happy to tell you that we just updated our Bioinformatics
journals section with cool new features !!!
1) A list of 20 Bioinformatics related journals. When it was possible
we associated to each journal, The web address, the impact factor, The
RSS/Feed address and a view at a glance of the articles of the current
issue.
2) The second sub-section contains a Google search engine that enables
you to perform a search restricted to these Bioinformatics journals.

The dedicated address is :
http://www.bioinformatics.fr/journals.php

And we made it printer friendly in case you want to read it during
your coffee break.

Hope you will enjoy it.
If your favorites bioinformatics journal is missing do not hesitate to
let us know.

Cheers,

The Bioinfomatics.fr team

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Google maps dedicated to Bionformatics jobs and Bioinformatics events

2007-06-08T00:39:21Z

Hi guys,

Just to let you know that we recently launched two Google maps
dedicated to Bioinformatics jobs and Bioinformatics events. So now it
will be very easy to check if there is an available position or an
upcoming event next to your place.
The two Google maps are available at the following address :

Bioinformatics job map :
http://www.bioinformatics.fr/jobs.php?mapview

Bioinformatics events map :
http://www.bioinformatics.fr/events.php?mapview

Kind Regards,

The Bioinformatics.fr team

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OPTIMIZER: a web server for optimizing the codon usage of DNAsequences.

2007-05-13T03:02:35Z

I wish to introduce the OPTIMIZER web-server that optimizes the codon usage of a gene to increase its expression level. This web-server is focused on the heterologous, or even homologous, gene expression in bacterial hosts. Two indices, CAI and ENc (effective number of codons), are used to measure the optimization process.
Three methods of optimization are available:
- The 'one amino acid - one codon' method.
- A guided random method based on a Monte Carlo algorithm.
-The ‘customized one amino acid - one codon’ designed to maximize the optimization with the fewest changes in the query sequence.
One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using the following pre-computed tables from more than 150 prokaryotic species under strong translational selection:
- Codon usage from a Predicted Group of Highly Expressed Genes.
- Codon usage from the Group of Ribosomal Protein Genes.
- tRNA Gene Copy Numbers (tGCN).
Additionally, codon usage tables from the Codon Usage database (CUTG) can also be used.
OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER .
For more details see the article Puigbo et al. 2007 Nucleic Acids Research, doi:10.1093/nar/gkm219 .

--------------------------------------------------------------------------------------------------------------------
Pere Puigbò Avalos, PhD Student
Evolutionary Genomics Group,
Biochemistry and Biotechnology Department,
Rovira i Virgily University.
C/Marcel·lí domingo s/n. 43007. Campus Sescelades. Tarragona.

Phone: 0034.977.55.84.86
Web Page: http://genomes.urv.cat
E-mail: ppuigbo@...
--------------------------------------------------------------------------------------------------------------------

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TOPD/FMTS: software to compare Phylogenetic trees

2007-05-09T09:18:26Z

I wish to introduce the TOPD/FMTS software to evaluate similarities and differences between phylogenetic trees. TOPD/FMTS can compare trees with leaf-sets that either completely or partially overlap and can be also used to compare two trees, one or both of which are multigene family trees.

The version 1.0 of TOPD/FMTS implements the following methods to compare phylogenetic trees:
- Split distance.
- Nodal distance.
- Disagree.
- Taxa in common.
- Quartets.
- Triplets.

Each option is also complemented with a randomisation analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation.

TOPD/FMTS is freely available at: http://genomes.urv.cat/topd .
For more details see the article Puigbo et al. 2007. Bioinformatics doi: 10.1093/bioinformatics/btm135 .

--------------------------------------------------------------------------------------------------------------------
Pere Puigbò Avalos, PhD Student
Evolutionary Genomics Group,
Biochemistry and Biotechnology Department,
Rovira i Virgily University.
C/Marcel·lí domingo s/n. 43007. Campus Sescelades. Tarragona.

Phone: 0034.977.55.84.86
Web Page: http://genomes.urv.cat
E-mail: ppuigbo@...
--------------------------------------------------------------------------------------------------------------------
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Medline Text Mining Web Service from the EBI

2007-04-12T15:38:13Z

Dear all,

Not so long ago I approached this list to announce a freely available
web based text mining tool called EBIMed, available from the European
Bioinformatics Institute:

http://www.ebi.ac.uk/Rebholz-srv/ebimed

A new service, Protein Corral, is available to provide protein to
protein interactions extracted from the literature:

http://www.ebi.ac.uk/Rebholz-srv/pcorral

If you would like to obtain Medline abstracts with XML annotations as
they come from EBIMed or Protein Corral, please visit Whatizit the
EBI's text mining web service accessible via any programming language
and very easy to use:

http://www.ebi.ac.uk/webservices/whatizit

--
________________________________________M.Arregui

Software Engineer, Rebholz group, Text Mining
European Bioinformatics Institute, Cambridge, UK

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QA-GEN Workshop - CFP, Sheffield, UK July, 22-23, 2007

2007-02-14T08:38:36Z

CALL FOR PAPERS
----------------------------------------------------------------------------------------------------------------------

QA-Gen Workshop

QA-gen Workshop: Quantitative approaches for knowledge discovery and
decision support in the post genomic era

In conjunction with the 15th International Conference on Conceptual
Structures (ICCS 2007)

22-27 of July, 2007, Sheffield Hallam University, UK

Call for Papers and Participation

Bioinformatics research is booming and genomics, proteomics or even
metabolomics are the words of the moment. It is the sequencing of the
human genome that is expected to bring about a major impact on the
prevention, diagnosis, treatment, monitoring, and outcome of several
diseases. Progress will most likely occur in a stepwise fashion with the
biggest initial impact in diagnosis and molecular targeting of new
medicines.

This abundance of new data, however, requires the combination of
statistical and machine learning techniques for the efficient extraction
of knowledge and analysis of data. Modelling, simulation, pattern
analysis, image analysis and data mining algorithms and techniques that
combine good performance both in terms of accuracy and computational
efficiency appear as a necessity if we want such systems to be put in
practice and to support clinical practice (diagnosis, prognosis,
treatment selection, drug design).

The goal of this workshop is to explore state-of-art approaches and
challenges on the field.

Topics

Topics to be addressed in the submissions, include (without being
limited to) quantitative analysis, knowledge based or artificial
intelligence applications in bioinformatics related to:

* Expression analysis
* Sequence analysis
* Structure prediction
* Image processing, quantification and analysis
* Web services and platforms
* Ontology engineering
* Simulation tools
* In-silico oncology
* Algorithms & tools to support knowledge discovery
* Models & tools to support clinical bioinformatics

Submission Details

Both contributions with a theoretical and a practical focus are welcome.
Papers could demonstrate algorithms and techniques related to
quantitative analysis and knowledge discovery in the bioinformatics
domain but also practical application and systems for related decision
support.

Papers will be reviewed for adherence to the workshop scope and quality
by the chairs and additional reviewers. Approximately 10-12 papers will
be selected for presentation. Accepted papers of appropriate quality
will be published in an ISBN numbered ICCS-2007 Workshop Volume by Springer.

Important Dates

* *Paper submission*:
o Directly to the workshop chairs via e-mail
o Deadline: April 4, 2007. 5-6 pages, in PDF format, following
the Springer LNCS rules <http://www.springer.de/comp/lncs>.
See the Workshops web site
* *Notification of acceptance*: April 15, 2007
* *Camera ready copy*: April 28, 2007
* *Workshop*: July, 22 and 23 of July 2007.

Program Chairs

* Yorgos Goletsis, University of Ioannina, Greece, Technical Manager
of MATCH project (e-mail: goletsis AT cc DOT uoi DOT gr)
* Costas Papaloukas, University of Ioannina, Greece (e-mail:
papalouk AT cc DOT uoi DOT gr)

Further Information

For further information on the workshop you can contact directly the
conference chair.

See the ICCS 07 website <http://www.iccs.info> for further information
on ICCS 2007.

You can contact the workshop organisers directly for any further
information.

The workshop is organised within the framework of MATCH project
<http://www.match-project.com> (IST-2005-027266) with the co-operation
of University of Patras <http://www.upatras.gr>, Sheffield Halam
University <http://www.shu.ac.uk> and University of Ioannina
<http://www.uoi.gr>.

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Re: [TE] MendelWeb 95.1

2006-09-28T10:44:39Z

"Lane Conn" <lconn@...> wrote:

>I'm looking for MendelWeb. Could you please help me locate this
>teaching resource.

How about using Google? Using this search engine gave me the following
(and somehow obvious) link: http://www.mendelweb.org/

Christian

--
X-no-Sig: yes

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[TE] MendelWeb 95.1

2006-09-28T09:20:57Z

Hello -
I'm looking for MendelWeb. Could you please help me locate this
teaching resource.

Thank you,

Lane Conn
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GATEWAY Cloning

2006-08-12T18:50:26Z

Dears
I am looking for a software in the internet to help me on GATEWAY cloning.
Have you any information about it?
Thanks!
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GenBank Search Engine

2006-07-11T17:44:25Z

Announcing a free GenBank Search Engine at
http://complexity.inbre.alaska.edu/swish.html

Features:
1) 2 intuitive basic query interfaces
2) 1 advanced query interface
3) programmatic access to the back-end

Thanks,

Jim

--

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
James Long
University of Alaska Fairbanks
Institute of Arctic Biology
jim.long|at|alaska.edu
(907) 474-6384
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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CFP: Algebraic Biology 2007

2006-07-06T01:19:27Z

[Apologies if you receive multiple copies]

******************************************************************
* *
* AB2007 *
* Second International Conference on Algebraic Biology *
* *
* July 2-4, 2007 *
* Castle of Hagenberg, Austria *
* *
* *
* http://www.risc.uni-linz.ac.at/conferences/ab2007/ *
* *
******************************************************************

AIMS AND SCOPE
==============

The Second International Conference on Algebraic Biology, AB'07, is an
international forum to promote discussion and interaction between
researchers who intend to apply symbolic computation - computer algebra
and computational logic - to various issues in biology.

The conference covers all aspects of applications of algebraic and
logic methods in biology, including, but not restricted to:

* polynomial methods
* group theoretical methods
* rewriting methods
* automated reasoning methods
* automata methods
* formal language methods
* combinatoric methods
* symbolic-numeric algorithms (sequential, parallel, distributed,
grid processing)

for

* mathematical modeling
* model identification
* system analysis and design
* system verification
* parameter fitting
* genome comparison
* sequence and structure analysis
* evolutionary analysis
* network inference
* optimization

and other problems in biology.

SUBMISSION
==========

Authors are invited to submit original papers that have not been submitted
for publication elsewhere. Submissions should be at most 15 pages including
references, prepared in LaTeX and formatted according to the Springer llncs
style (http://www.springer.de/comp/lncs/authors.html). Additional material
intended for the referees but not for publication in the final version may
be placed in a clearly marked appendix that is not included in the page limit.

Submitted papers will be peer-reviewed, and the accepted papers will appear
in the proceedings before the Conference. We are currently negotiating with
Springer to publish the proceedings within the Lecture Notes in Computer
Science (LNCS) series.

DATES
=====

December 4, 2006: Deadline for registration of abstracts.
December 11, 2006: Deadline for submission of full papers.
March 5, 2007: Notification of acceptance/rejection.
April 2, 2007: Camera-ready paper submission.
July 2-4,2007: Conference.

INVITED SPEAKERS
================

Reinhard Laubenbacher, Virginia Bioinformatics Institute (USA)
Bud Mishra, New York University (USA)
Gheorghe Paun, Institute of Mathematics of the Romanian Academy (Romania)

CONFERENCE CHAIRS
=================

Hirokazu Anai, Fujitsu Laboratories Ltd (Japan)
Bruno Buchberger, Johannes Kepler University of Linz (Austria)
Hoon Hong, North Carolina State University (USA)
Katsuhisa Horimoto, National Institute of Advanced Industrial Science and Technology (Japan)

PROGRAM CHAIRS AND PROCEEDINGS EDITORS
=====================================

Hirokazu Anai, Fujitsu Laboratories Ltd. (Japan)
Katsuhisa Horimoto, National Institute of Advanced Industrial Science and Technology (Japan)
Temur Kutsia, Johannes Kepler University of Linz (Austria)

PROGRAM COMMITTEE
=================

Tatsuya Akutsu, Kyoto University (Japan)
Hirokazu Anai, Fujitsu Laboratories Ltd. (Japan), PC Co-Chair
Michael P. Barnett, Princeton University (USA)
Bruno Buchberger, Johannes Kepler University of Linz (Austria)
Vincenzo Capasso, Universita degli studi di Milano (Italy)
Gautam Dasgupta, Columbia University (USA)
Francois Fages, INRIA Rocquencourt (France)
Shinji Hara, University of Tokyo (Japan)
Sepp Hochreiter, Johannes Kepler University of Linz (Austria)
Hoon Hong, North Carolina State University (USA)
Katsuhisa Horimoto, National Institute of Advanced Industrial Science and Technology (Japan), PC Co-Chair
Hans Irschik, Johannes Kepler University of Linz (Austria)
Temur Kutsia, Johannes Kepler University of Linz (Austria), PC Co-Chair
Enno Ohlebusch, University of Ulm (Germany)
Stanly Steinberg, University of New Mexico (USA)
Bernd Sturmfels, University of California at Berkeley (USA)
Carolyn L. Talcott, SRI International (USA)
Ashish Tiwari, SRI International (USA)
Jens Volkert, Johannes Kepler University of Linz (Austria)
Dongming Wang, Beihang University (China) and UPMC-CNRS (France)
Kazuhiro Yokoyama, Rikkyo University (Japan)
Ruriko Yoshida, Duke University (USA)

WEB PAGE
========
http://www.risc.uni-linz.ac.at/conferences/ab2007/

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Accelerated Bioinformatics Data Processing Solutions

2006-06-26T21:21:04Z

Hi,
Just a note to let the community know of a new product - the BioBoost
from Progeniq - which accelerates computationally intensive
bioinformatics applications, at up to 50x-100x faster than on a typical
workstation processor. The BioBoost uses Field Programmable Gate Array
(FPGA) technology on a USB 2.0 or PCI based device, to accelerate
applications at
significantly lower cost.
Do let me know if this may be of assistance to anyone, I'll be happy to
get in touch.
Cheers, Tali
www.progeniq.com
e-mail:tali@...

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Re: biology video resources

2006-06-17T18:43:22Z

On Sun, 11 Jun 2006 00:56:52 +0800, "Fan Cheung"
<cecilia801537@...> wrote:

>I am a novice in this forum. Can anybody tell me where i can download
>visual resources on biology for free?Thank you.

They are spread around.

Suggest you google on a specific topic of interest to you, and include
a search term such as video or animation. You'll find things.

bob

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[DI] Wanted: Physiology software for teaching

2006-06-12T10:56:23Z

Dear Sir,

I am looking for a physiology software, to teach physiology.

You can e-mail Dr. Maniram Ramoutar at drmaniramoutar@...

Thank you

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biology video resources

2006-06-10T10:56:52Z

I am a novice in this forum. Can anybody tell me where i can download
visual resources on biology for free?Thank you.

--
Yours, sincerely
Fan Cheung

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An Open Content Directory for the Life Sciences and Medical Sciences

2006-06-02T03:55:27Z

An Open Content Directory for the Life Sciences and Medical Sciences

Jon Rees PhD, Oxford Informatics Ltd, the Open Content Company for Life
Sciences and Medical Sciences, 49, Swinburne Road, Oxford
Tel: 44 (0) 79 70 89 33 71, E-mail: jon.rees@...

BioDirectory is a new online resource for Life Scientists and Medical
Scientists which is a uniquely "open content" database of tools,
databases and resources of value to the scientific community both in
academia and industry.

The BioDirectory contains resource information aggregated from
Bioinformatics.Net and the life and medical sciences parts of Open
Directory, creating a definitive directory containing more than 7950
categories containing 34500 entries.

Whereas the Open Directory may contain around 16.5% bad links,
including perhaps about 11.4% dead links [1,2], the BioDirectory data
(both public feed and web site) excludes dead links each time the
directory is re-built fortnightly, improving the user's experience.

The automated curation of entries is facilitated by a web crawler,
BioZilla, which spiders through a subject-specific tunnel of life
science and medical sciences web sites, while a search engine has also
been created to allow users to full-text search across more than 86,000
web resources (fast growing), with more results and more relevant
results than are provided by the Open Directory search facility.

There is an ongoing effort to interlink life sciences informatics,
bioinformatics, cheminformatics and medical sciences informatics
categories to the relevant categories to integrate access to knowledge
about subjects, species, and clinical areas with the resources, tools
and databases which can be used to study them

Example: "Nematodes" and "Nematode zoonoses" - the BioDirectory section
on nematodes is linked both to a section on nematode genomics, as well
as a further medical section on nematode zoonoses.

A key goal for BioDirectory is to interlink information on subjects
written from biological, medical and technological perspectives, which
provides alternative routes into knowledge bases for scientists-in-
training, from undergraduates through to post-doctoral scientists.

There is also an on-going effort to create starting points for research
in several new technology areas, which will be announced through our
newsletter as they are launched.

BioDirectory features a search engine with better results than Open
Directory search, and an easier to navigate structure and accessible
design than BioWareDB [3]

An important feature is that BioDirectory is Open Content, so that both
scientists and the general public can contribute, learn, share and
research freely.

OpenContent's only excuse for existing is to "facilitate the prolific
creation of freely available, high-quality, well-maintained Content."
This Content can then be used in an infinity of ways, restricted only
by the imagination of the user. One of the most significant uses may be
supporting instruction and helping people learn. Every section of
BioDirectory is available as an RSS feed.[5]

I look forward to hearing your constructive feedback on this new
endeavour, including your suggestions as to how we can best turn this
in to an online community, and how to extend the availability of the
content.

http://www.biodirectory.com/

Best wishes,

Jon Rees

PS. Since opening the site to the public on May 7th 2006, more than
25,000 user visits have been recorded.

References

[1] Percentage of dead links was determined from a random sample of
1000 taken from the Life and Medical Sciences subsection of the Open
Directory as measured by our web crawler, using a 12 hour old RDF dump
from http://rdf.dmoz.org
[2] So much for the ODP then? An article by Phil Craven from
http://suo.ieee.org/email/msg13230.html
[3] Matthiessen MW. 2003. BioWareDB: the biomedical software and
database search engine. Bioinformatics. 2003 Nov 22;19(17):2319-20.
[4] Fox JA, Butland SL, McMillan S, Campbell G, Ouellette BF. 2005. The
Bioinformatics Links Directory: a compilation of molecular biology web
servers. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W3-24.
[5] OpenContent.org

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