Nabble - Bio.net - Bio-soft

Unipro UGENE v1.6 is released

2009-12-23T22:16:17Z

Unipro UGENE is a free open source multiplatform software tool for
molecular biologists.

Version 1.6 new plugins:

* Phylip plugin for building phylogenetic trees. Based on original
Phylip 3.6 package .
o Neighbor Joining algorithm;
o Phylogenetic trees visualization;
o Integration with Multiple Alignment Editor.

* Distributed computing in UGENE
o Support for launching HMMER 3, Smith-Waterman, MUSCLE
tasks on remote machines.
o Remote tasks support;

New features and bug fixes:

* Search for tandem repeats added introduced in Repeat Finder
plugin;
* Project files transferability support;
* "Export project" feature;
* Remote databases interaction: NCBI, PDB, Swiss Prot;
* BioStruct3D plugin: anaglyph stereo mode;
* and a lot more...

Prebuilt packages for different platforms and complete source code is
available here: http://ugene.unipro.ru/download.html

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Problem facing at writing a script to run multi-fasta sequence in fgenesh

2009-12-10T01:52:12Z

Hi,

I just try to write a script to allow fgenesh to run multi-fasta sequence.
Unfortunately I faced the problem when I writing it :(
My purpose is tried to write a script that allows the following command
worked perfectly:
./script_for_multi_fasta Program Par_file Seq_file <Other options>
eg.
./run_program.pl fgenesh Human fileseq -pmrna > fileres
Thanks a lot for any suggestion and advice.
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Trend in Bioinformatics

2009-12-07T07:29:10Z

Dear Colleagues
It is important for all bioinformaticians to know the need of
biologist as our major role is to assist biologist in solving their
problem. There is a need of better coordination between user
(biologist) and service providers (bioinformaticians). Please give
your input, your input is important for the development of the field.

Our group is working in the filed of bioinodmatics ( http://www.imtech.res.in.raghava/
). We are interested to know the trend in bioinformatics, I mean what
are the hot problems one should address. We have capability to develop
databases, software and web services, we wish to address new and
challenging problems. I will highly appreciate if members of this
group suggest major challenges faced by researchers working in the
filed of biology/pharma which bioinformaticians can
address. Thanks for your help.

Raghava

======================================================
# Dr G P S Raghava (FASc, FNASc), Head Bioinformatics Centre #
# Institute of Microbial Technology, Sector-39A, Chandigarh, India #
# Phone: +91-172-2690557, Fax: +91-172-2690632
#
# Eadd: http://www.imtech.res.in/raghava/ ragh...@... #
#=====================================================

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GMOD Community Meeting, January 2010

2009-11-25T13:11:27Z

The next GMOD meeting will be held January 14-15 in San Diego, California,
USA, immediately after the Plant and Animal Genome (PAG) conference. There
is no registration fee for this meeting. However, there is limited space, so
please register early. See the meeting page for more information:
http://gmod.org/wiki/January_2010_GMOD_Meeting.

GMOD is a collection of interoperable open source software components for
visualizing, annotating, and managing biological data. GMOD is also a
community of users and developers asking diverse questions, and facing
common challenges, with their biological data. GMOD has many widely used
software packages, including GBrowse, Apollo, CMap, Chado, BioMart, MAKER,
Galaxy, Textpresso, and many others. The availability and affordability of
next generation sequencing (NGS) has made GMOD particularly timely to a wide
range of research groups.

As with previous GMOD meetings, there will be a mixture of project,
component, and user talks. There will also be a number of satellite meetings
focusing on particular areas of interest.

Thanks,

Dave Clements
GMOD Help Desk

--
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
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Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery

2009-11-19T14:32:08Z

Dear All,

MolSoft LLC ( www.molsoft.com ) and q.e.d. life science discoveries,
inc., are conducting a joint two day workshop on Dec 14-15, 2009 at the
Molsoft LLC facility in La Jolla, CA USA entitled "Modern Drug Target
Crystallography and Structure Based Drug Design".

The course will be taught by two experts in the field: Dr. Bernhard
Rupp, crystallography textbook author and president of q.e.d. life
science discoveries, and Dr. Ruben Abagyan, founder of Molsoft LLC
and Professor of Pharmacology at the University of California San Diego,
Skaggs School of Pharmacy and Pharmaceutical Sciences.

The provided course materials include a copy of the new and highly
acclaimed textbook Biomolecular Crystallography: Principles, Practice,
and Applications to Structural Biology.

For more information please see:
http://www.ruppweb.org/workshops/Molsoft_2009.htm

--
Andrew Orry Ph.D.
Senior Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla, CA 92037
U S A

Phone: (858) 625-2000 (x108)
Fax: (858) 625-2888
www.molsoft.com
Latest ICM News: www.molsoft.com/news.html

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HBPLUS v 3.03 - Hydrogen Bond Calculator

2009-11-11T03:16:47Z

Hello,

I would like to have a copy of the Hbplus software, I was about to send
a normal courier letter with the license agreement but I saw that the
page was generated on 1994 so I'm not sure if this is the way to proceed.
Could you please help me?

Thanks a lot and sorry for the inconveniences,
j

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Re: GeneJockey

2009-10-24T07:12:04Z

MehdiM <mehdi.mpour@...> wrote:
> Hi,

> Our group has used the GeneJockey for sequence analysis in the past.
> Now that the program is no longer supported, we need to be able to use
> the files generated by GeneJockey in other programs. How do I do that?
> I have copied the files to another computer and tried to change the
> file format by changing the extension (suffix) to others and tried to
> open with CLC workbench, but it failed. Converting to .txt generated
> strange figures and letters. Are we doomed to keep the old Mac with
> the old program for ever?

Well, changing the extension of a file does not magically convert it to another
format. If you cannot find a programm that understands the files created by
your old software you will have to open them with the old program and export
to a more generally understood format (assuming that GeneJockey is able to
export to other formats).

cu
Philipp

--
Dr. Philipp Pagel
Lehrstuhl f. Genomorientierte Bioinformatik
Technische Universität München
http://webclu.bio.wzw.tum.de/~pagel/

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GeneJockey

2009-10-23T11:56:48Z

Hi,

Our group has used the GeneJockey for sequence analysis in the past.
Now that the program is no longer supported, we need to be able to use
the files generated by GeneJockey in other programs. How do I do that?
I have copied the files to another computer and tried to change the
file format by changing the extension (suffix) to others and tried to
open with CLC workbench, but it failed. Converting to .txt generated
strange figures and letters. Are we doomed to keep the old Mac with
the old program for ever?

Thanks for all the help!!!

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InterMine workshop, Cambridge UK

2009-10-23T07:01:53Z

Dear all,
We still have some places available on an InterMine workshop we
are running in Cambridge, UK on November 16th-17th.

InterMine is a free, open source system for integrating biological
data and querying it via a powerful webapp and query API.

http://www.intermine.org

InterMine is used to build FlyMine (http://www.flymine.org) and is now
being deployed at the yeast, rat and zebrafish model organism databases.

The course is intended for software developers and will give a complete
introduction to setting up an InterMine system. It is free to attend,
more details and sign up information are available here:

http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html

Please get in touch if you have any questions.

Regards,
Richard.

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Last Call for Papers: 2010 IEEE International Symposium on Biomedical Imaging (ISBI)

2009-10-23T02:26:00Z

************************** CALL FOR PAPERS **************************

2010 IEEE International Symposium on Biomedical Imaging (ISBI)

To be held 14-17 April 2010, Rotterdam, The Netherlands

Four-page paper submission deadline: 2 November 2009 !!!

NEW: Best Student Paper Awards (see below)

See http://www.biomedicalimaging.org/ for details

The IEEE International Symposium on Biomedical Imaging (ISBI) is the
premier forum for the presentation of technological advances in
theoretical and applied biomedical imaging. ISBI 2010 will be the
seventh meeting in this series. The previous meetings have played a
leading role in facilitating interaction between researchers in
medical and biological imaging. The 2010 meeting will continue this
tradition of fostering crossfertilization among different imaging
communities and contributing to an integrative approach to biomedical
imaging across all scales of observation.

ISBI is a joint initiative of the IEEE Engineering in Medicine and
Biology Society (EMBS) and the IEEE Signal Processing Society (SPS).
The 2010 meeting will feature an opening morning of tutorials,
followed by a scientific program of plenary talks, special sessions,
and oral and poster presentations of peer-reviewed contributed papers.

Confirmed plenaries: New clinical imaging technologies (Richard
Ehman); Challenges in bioimage informatics (Jason Swedlow); Molecular
imaging and applications (Clemens Lowik); Challenges in biomedical
image analysis (Milan Sonka). Special Sessions: fMRI & DTI (Carl-
Fredrik Westin); High-field clinical MRI (Andrew Webb); Fluorescence
guided surgery (Vasilis Ntziachristos); Whole-body imaging and
analysis (Faiza Admiraal); Histological and intravital microscopy (Tom
Vercauteren); Ultrasound imaging and analysis (Hans Bosch); Multi-
parameter biomedical optical imaging and analysis (Atam Dhawan and
Metin Gurcan); Computer aided diagnosis (Nico Karssemeijer).
Tutorials: Biomedical image registration (Gustavo Rohde and Graeme
Penney); Optical microscopy and deconvolution (Hans van der Voort and
Erik Manders); Ultrasound imaging and therapeutics (Elisa Konofagou
and Constantin Coussios); Machine learning for biomedical image
analysis (Marco Loog and David Tax).

Contributed Program:
High-quality papers are solicited describing original contributions to
the mathematical, algorithmic, and computational aspects of biomedical
imaging, from nano- to macro-scale. Topics of interest include image
formation and reconstruction, computational and statistical image
processing and analysis, dynamic imaging, visualization, image quality
assessment, and physical, biological, and statistical modeling. Papers
on molecular, cellular, anatomical, and functional imaging modalities
and applications are welcomed. All accepted papers will be published
in the proceedings of the symposium and will be available online
through the IEEE Xplore database.

Best Student Paper Awards:
ISBI 2010 awards a prize for best student paper, as judged by a
special award committee. At most three papers will be awarded a prize
of 500 euro each. A paper is eligible if the primary author is a
student at the time of paper submission and this person will indeed
present the paper at the symposium if it is accepted.

Important Dates:
Deadline for submission of 4-page paper: November 2, 2009
Notification of acceptance/rejection: January 15, 2010
Submission of final accepted 4-page paper: February 15, 2010
Deadline for author registration: February 15, 2010
Deadline for early registration: March 1, 2010

*********************************************************************

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CMC 2010 Shenzhen China: Extended Deadline 15 November

2009-10-21T11:56:17Z

2nd International Conference on Communications and Mobile Computing
(CMC 2010)

April 12-14, 2010

Shenzhen, China

http://world-research-institutes.org/conferences/CMC/2010
http://world-research-institute.org/conferences/CMC/2010

Call for Papers & Expo

CMC 2010 intends to be a global forum for researchers and
engineers to present and discuss recent advances and new
techniques in communications and mobile computing. We invite
you to submit your original papers on the most recent results
and technology trends to one of the 5 symposiums. Due to numerous
requests, the submission deadline is extended to 15 November 2009.

CMC 2010 conference proceedings will be published by the IEEE
Computer Society's Conference Publishing Services (CPS) which
will include the conference proceedings in the IEEE Xplore and
submit to Ei Compendex and ISTP for indexing (CMC 2009 proceedings
were already indexed in Ei).

CMC 2010 is organized by the College of Information Engineering,
Shenzhen University, China. In addition to research papers, CMC
2010 also seeks exhibitions of modern products and equipment for
communications and mobile computing.

Shenzhen, situated just across the border from Hong Kong, is a
beautiful coastal city in southern China. It is a showcase of
China’s reforms and opening up to the rest of the world. In 27
years, Shenzhen has developed from a small fishing village into a
modern city with a population of 12 million and a gross domestic
product (GDP) ranking among the highest in China. Famous tourist
attractions include Dapeng Fortress, Lotus Hill, Shennan
Thoroughfare, and Yangtai Mountain.

If you have any questions, please email us at
cmc2010 <AT> szu.edu.cn
or call +86 755 2653 6198 or +86 755 2653 5259.

Important Dates:

Paper Submission Deadline: 15 November 2009
Review Notification: 10 December 2009
Final Papers and Author Registration Deadline: 30 December 2009

*** Please forward to those who may be interested. ***

(To unsubscribe, please reply with the email subject being
"Unsubscribe bio-soft@...".)
(Thanks and apologies)

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Secondary Structure and Surface Accessibility predictions easily made

2009-10-07T12:41:53Z

Hi Everyone,
I have seen that many people are interested in Secondary Structure
predictions, and
also interested in the surface of proteins.

I therefore want to bring your attention to a paper I have recently
published, which has the title: A generic method for assignment of
reliability scores applied to solvent accessibility predictions.,

which is freely available here: http://www.biomedcentral.com/1472-6807/9/51

It describes a new method, which is implemented in our freely
available method: NetSurfP:
http://www.cbs.dtu.dk/services/NetSurfP/

Basically it predicts the secondary structure of a protein, its
surface accessibility and also the reliability of surface
accessibility prediction in form of a z-score :-)

I hope you will find it useful in your research :-)

Best Regards,

Bent Petersen, Ph.D Student, M.Sc.

Center for Biological Sequence Analysis - CBS
Department of Systems Biology,
Technical University of Denmark.
Bld. 208, DK-2800 Lyngby, Denmark

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Adopting R&D Informatics Systems

2009-10-01T12:41:03Z

Hello,

For those who may be interested in the above topic, my company,
Cambridge Healthtech Institute, has organized a 3-day conference that
will be held on February 3-5, 2009 in San Francisco, CA. For details
and to register, go to
http://www.tri-conference.com/ird.asp

Please contact me with any questions.

Best regards,

James Prudhomme
Cambridge Healthtech Institute
Tel: 781-972-5486
jprudhomme@...

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Perl-SQL-WebServices workshop at CBS-DTU

2009-09-28T20:52:42Z

EMBRACE Workshop on Perl, SQL and Web Services, CBS, November 16-20, 2009
The workshop will be held at the Center for Biological Sequence Analysis
(CBS), Technical University of Denmark.

The workshop is intended to give the participant an introduction to a set
of skills needed to perform basic bioinformatics work without the assistance
of professional programmers. It will cover a general-purpose scripting
language (Perl), database manipulation (SQL) and programmatic access to
remote resources (Web Services). Brief introductory lectures will be
followed by extensive hands-on exercises aiming at the ability to develop
clean, efficient Perl scripts accessing relational databases and remote
resources. There will be template scripts to take home and develop further
in the context of the participant's own work.

The workshop is open to everybody, free of charge. PhD students can receive
credits for participation (for details please consult Dorthe Kjaersgaard at
dorthek@...).

For registration and more information please see the workshop page:

http://www.cbs.dtu.dk/courses/embrace/2009-11-16/

Registration deadline is on September 30, 2009.

Kristoffer Rapacki

------------------------------------------------------------------------
Kristoffer Rapacki Center for Biological Sequence Analysis
phone: +45 4525 2483 Department of Systems Biology
fax: +45 4593 1585 Technical University of Denmark
Building 208
e-mail: rapacki@... DK-2800 Lyngby Denmark
------------------------------------------------------------------------

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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-09-25T16:17:18Z

The 7th Georgia Tech - ORNL Conference on Bioinformatics -
In silico Biology: Genome Biology and Bioinformatics
will be held in Atlanta, Georgia, November 12-14, 2009
http://www2.isye.gatech.edu/binf2009/

Georgia Tech continues the tradition of organizing bi-annual
International Conference on Bioinformatics, bringing together leading
researchers in genomics, bioinformatics and genome biology to present
recent advances in the field and to discuss open problems.

Important Dates

Deadline for early registration: October 15, 2009
Deadline for poster abstract subsmission: October 1, 2009
Notification of acceptance of abstracts: October 11, 2009

We invite papers submissions in the following areas
* genomics
* transcriptomics
* proteomics
* reconstruction and modeling of gene networks
* evolutionary biology

SPEAKERS

Margaret O. Dayhoff lecture:

David Lipman , NCBI/NIH, Bethesda, MD, USA

Plenary Speakers:

Vineet Bafna, University of California at San Diego, USA
Gill Bejerano, Stanford University, Stanford, CA, USA
Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Nick Grishin, University of Texas, Dallas, TX, USA
Curtis Huttenhower, Harvard University, Boston, MA, USA
King Jordan, Georgia Tech, Atlanta, GA, USA
Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA
Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
Boris Lenhard, University of Bergen, Norway
Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel
Joanna Masel, University of Arizona, Tucson, AZ, USA
Andrey Mironov, Moscow State University, Russia
Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Natasa Przulj, University of California at Irvine, CA, USA
John Reinitz, State Uiversity of New York at Stony Brook, NY, USA
Pierre Rouze, Gent University, Gent, Belgium

CONFERENCE CHAIRS
Mark Borodovsky, Georgia Tech and Emory University
Eva K. Lee, Georgia Tech and Emory University

PROGRAM COMMITTEE
Nicholas Bergman, Georgia Tech
Dmitrij Frishman, Technische Universitaet Muenchen, Germany
Andrey Gorin, Oak Ridge National Laboratory
Andrzej M. Kierzek, University of Surrey, UK.
Eileen Kraemer, University of Georgia
Jun Liu, Harvard University
Hannah Margalit, Hebrew University
Andrey Rzhetsky, University of Chicago
Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute
Gary Stormo, Washington University
Lance Waller, Emory University
Ying Xu, University of Georgia and Oak Ridge National Laboratory
Soojin Yi, Georgia Tech
Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee

ADMINISTRATION
Harry Sharp, Georgia Tech

CONFERENCE LOCATION

The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus
is located in Midtown Atlanta near the center of the 1996 Olympic
development, close to the Fox Theatre and Margaret Mitchell house.

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Professional development through distance learning

2009-09-20T23:30:42Z

At the University of Manchester, UK, we have over 10 years experience in
providing advanced, multidisciplinary, training to participants from a
range of backgrounds, including Biology, Healthcare, Medicine and
Computer Science. These courses are designed to enable biologists and
computer scientists to update their skills while remaining in the
workplace. Our distance courses 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 to software development in Java
- Theory and Applications in Bioinformatics

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 module options, please contact
Heather.Vincent@...

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Software to display genetic and geographical relationships - any suggestions?

2009-09-17T02:13:07Z

Hi,

I have some viral sequences from around the world. When I construct
dendrograms they suggest a geographical relationship in the clustering
of the sequences. Is there any software I can use which could
simultaneously analyse genetic distances AND geographical distances to
represent the clustering I can see. I had thought of principal
co-ordinate analysis (PCA), but if there is something out there designed
to do this sort of thing that would be better.

Any suggestions (including how I could do a PCA on these data) would be
gratefully received.

Vince

Vincent Mulholland
Science and Advice for Scottish Agriculture (SASA)

SASA is a Division of the Scottish Government Rural Payments and
Inspections Directorate

Correspondents should note that all communications to or from SASA (Science and Advice for Scottish Agriculture a Division of the Rural Payments and Inspections Directorate of the Scottish Government) may be automatically logged, monitored and/or recorded for lawful purposes.

The original of this email was scanned for viruses by the Government Secure Intranet (GSi) virus scanning service. On leaving the GSi this email was certified virus-free.

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Scoring of AFLP bands

2009-09-15T19:28:09Z

Hi
I want to know about analysis of AFLP gels using some statistical
software. Can any body guide me about co-dominant scoring of AFLP
bands. Many thanks in advance.
Regards
Faiz

FAIZ-UL-HASSAN
Lecturer
Department of Animal Breeding and Genetics
University of Agriculture, Faisalabad, Pakistan
Phone 00 92 41 9200161-70 Ext. 3202
Cell 00 92 333 8317328

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Handling NA's in REST 2008 software

2009-09-14T15:35:37Z

Hello,

Can any PCR data analysis experts in the forum please answer this question ?

How does one handle NA's (unknown data items) while analysing PCR data
using REST 2008 software ?

NA are not accepted by the program. While zeros are accepted, I suspect, the results are not correct if zeros are used instead of NAs.

Thanks
Suki
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Scientific Dictionary for MS Word

2009-08-20T08:46:05Z

Hi,

I came across a forum article written in 1996 saying that you are working on a Microsoft Word dictionary for biologists, having already made one for "chemistry and biochemistry, and organic.". I don't suppose you've done this and can forward me a copy, please?? Actually a generic "scientist" dictionary would be ideal for me, as I did my initial degree in (Joint Honours) Chemistry & Physics, and now do computational biology.

The article I found is here:-
http://www.bio.net/bionet/mm/bio-soft/1996-April/014002.html

What's the chances you don't use this e-mail address any more....? :(

I'd really appreciate it, for reasons I'm sure you already know and can relate with!

Kind regards,
Alex Leach
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batch query

2009-08-15T05:07:06Z

Hi there,
i want to use BLINK at NCBI in batch query mode. Does anybody has
perlscript to do so. I would be very grateful if soomeone share it
with me.
regards
sanjay

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Introduction to Bioinformatics, October 2009

2009-08-06T09:10:08Z

The online course, Introduction to Bioinformatics, from The University
of Manchester, will begin again in October 2009. Like all our distance
courses it is delivered in a Virtual Learning Environment, which allows
us to extend the classroom into the web. We use a range of tools to
support our online teaching activities.

Each course, which is paced to suit those in full-time employment, runs
over 16 teaching weeks.

Teaching and learning are focussed around tutor-supported exercises. In
this course, participants work together on the interpretation of their
results, before receiving feedback from the course tutor.

Week 1 Introduction to distance learning
Bioinformatics as a knowledge-based discipline

Weeks 2 and 3 Introduction to the sequence databases
Quality, redundancy and annotation
Sequence retrieval exercise and group discussion

Weeks 4 and 5 Nucleic acid sequence analysis

Weeks 6 and 7 Independent research and assessment

Weeks 8 and 9 Sequence alignment and database search
1. use of BLAST and FASTA, choosing suitable options;
2. interpretation of the results.

Weeks 10 and 11 Protein function prediction.

Weeks 12 and 13 Protein structure prediction
Practical exercise and group discussion

Weeks 14 to 16 Independent research and work on the second assessment

You will find information on all our courses, 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 module options, please contact
Heather.Vincent@...

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About Interproscan

2009-08-06T07:36:27Z

Hi Dale,
I am Manuel Cano, I work for one of the biggest coffee research centers in
Colombia at the Bioinformatics department and now I am trying to install
Interproscan in some of the machines we use here, but I am getting an error
(which I saw on a
forum<http://www.bio.net/bionet/mm/bio-soft/2005-January/024363.html>
of
yours) when I test it, so I was wondering if you solved the problem and how
did you do so?

This is the message:

pijao:bin sge$ ./iprscan -cli -i ../test.seq -iprlookup -goterms
SUBMITTED iprscan-20090806-09271322

FAILED
Iprscan job iprscan-20090806-09271322 failed and exit with status
code 256
./iprscan:
/Users/sge/opt/iprscan/tmp/20090806/iprscan-20090806-09271322/iprscan-20090806-09271322.xml
unavailable : No such file or directory
/Users/sge/opt/iprscan/bin/iprscan_wrapper.pl: failed to send error to
administrator: no destination address
Tool: iprscan
JobID: iprscan-20090806-09271322
Time: Thu Aug 6 09:27:13 2009
Error:

I would appreciate if you can help me with this because there is not much
information about it on the net.

Thanks in advance

Sincerely

--
Manuel Fernando Cano Montes.
Systems and Telecommunications Engineer
University of Manizales.
Alumnus AIESEC Manizales, Colombia
Bioinformática department
Cenicafé (Centro Nacional de Investigaciones de Café) - FNC
E-mail: manuel.cano@...
Tel: +57 3218169084
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Please help to test new mtDNA analysis software

2009-08-03T10:28:31Z

Hello Dear Colleagues!
We are currently developing a new automating mtDNA analysis software,
and are in great need in your competent opinion and feedback.
Our team would be really grateful to you, if you could give us some
criticism (or maybe even praise).

The program currently runs under MS Windows OS and requires
Microsoft .net framework 2.0 to be installed on your computer.
It works with *.ab1 files and is doing it quite well (as we hope :) )
If you would be so kind to help in testing - please email me to
mitotyper@... for i could send you a license key, or just post
your email in reply.

Download link is http://rapidshare.com/files/262683748/Mitotyper.msi.html

Thank you very much,
Alexey.

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GMOD Community Meeting, 6-7 August, 2009, Oxford UK

2009-07-17T21:02:31Z

There will be a GMOD Community Meeting, 6-7 August, 2009 at the University
of Oxford, in Oxford, UK.

GMOD (http://gmod.org) is a collection of interoperable, open-source
software components for managing, visualizing, annotating, and sharing
biological data. GMOD is also a community of users and developers
addressing common challenges with their biological data. The popularity of
next generation sequencing and other high-throughput methods has made this
GMOD meeting particularly timely.

GMOD meetings are an excellent opportunity to learn best practices from
other researchers, to meet GMOD users and developers, and to learn and
affect what is coming in the project. As with previous meetings, there will
be a mixture of project talks, component-focused talks, and user talks.

Registration for the meeting is now open and space is available on a first
come, first served basis. Attendance is limited to the first 55 people to
register. The meeting cost is £50.

See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more.

Please join us in Oxford this August.

Cheers,

Dave Clements
GMOD Help Desk

--
Register now for the August GMOD Meeting:
http://gmod.org/wiki/August_2009_GMOD_Meeting
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Re: DNA sequence editor

2009-07-09T03:41:16Z

dawe wrote:
> Astala Vista <rwmd1@...> wrote:
>
>> In common with many other sites, we are no longer providing GCG to our
>> users as it is increasingly more difficult to support. However, we need
>> a simple DNA sequence editor replacement for GCG SeqEd.
>>
>> We are running openSuSE 11.1. Any suggestions?

I am interested in adding something to EMBOSS, but afraid of the effort
involved if it needs significant further development.

I spent 2 solid years inside GCG's SeqEd converting it into an
EMBL/GenBank/SwissProt feature table editor for EGCG.

> If you find any, please let me know.
> Meanwhile you may try ApE:
>
> <http://www.biology.utah.edu/jorgensen/wayned/ape/>
>
> which is multiplatform

Useful to see a plasmid editor.

What is the license for ApE?

regards,

Peter Rice

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Re: DNA sequence editor

2009-07-08T11:42:39Z

Astala Vista <rwmd1@...> wrote:

> In common with many other sites, we are no longer providing GCG to our
> users as it is increasingly more difficult to support. However, we need
> a simple DNA sequence editor replacement for GCG SeqEd.
>
> We are running openSuSE 11.1. Any suggestions?

If you find any, please let me know.
Meanwhile you may try ApE:

<http://www.biology.utah.edu/jorgensen/wayned/ape/>

which is multiplatform

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DNA sequence editor

2009-06-22T02:00:52Z

In common with many other sites, we are no longer providing GCG to our
users as it is increasingly more difficult to support. However, we need
a simple DNA sequence editor replacement for GCG SeqEd.

We are running openSuSE 11.1. Any suggestions?

Many thanks,

Raymond

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Re: HCA-PLOT software

2009-06-18T06:34:52Z

Hi,

as far as I know, there is no downloadable tool. However, have a look at
this URL:
http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA

Regards,
Patrick
--
Korilog SARL
BP 34, 56190 Muzillac, France
Phone: +33 (0)960 368 038
Fax: +33 (0)297 428 820
web: www.korilog.com

Heng Xiang a écrit :
> Hello,
>
> Would you mind telling me if there are HCA-Plot softwares runing under Win
> or Unix, and where I can download them. Thanks very much.
> Heng xiang
>

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Re: HCA-PLOT software

2009-06-18T05:21:36Z

Did you mean the "Hydrophobic Cluster Analysis"?

I got the following link from ExPASy's Tools page:
http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA

On Jun 18, 11:14 am, Heng Xiang <hxiang....@...> wrote:

> Hello,
>
> Would you mind telling me if there are HCA-Plot softwares runing under Win
> or Unix, and where I can download them. Thanks very much.
> Heng xiang
>
> --
> Heng Xiang
>
> The Key Sericultural Laboratory of Agricultural Ministry of China,
> Southwest University, Chongqing 400715, China.
> Tel: +86 23 68251088
> Fax: +86 23 68251128
> E-mail: hxiang....@...

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HCA-PLOT software

2009-06-17T20:14:29Z

Hello,

Would you mind telling me if there are HCA-Plot softwares runing under Win
or Unix, and where I can download them. Thanks very much.
Heng xiang

--
Heng Xiang

The Key Sericultural Laboratory of Agricultural Ministry of China,
Southwest University, Chongqing 400715, China.
Tel: +86 23 68251088
Fax: +86 23 68251128
E-mail: hxiang.swu@...
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RE: Data structure for protein

2009-06-07T10:32:24Z

Your best bet is PDB format. Google it up, it gives coordinates and such for each aa.

-----Original Message-----

Message: 1
Date: Sun, 07 Jun 2009 06:57:35 +0100
From: Sujita Purushothaman <sujita@...>
Subject: [Bio-software] Data Structure for protein
To: bio-soft@...
Message-ID: <4A2B56CF.10102@...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,
I'm writing a program which has to hold information about the 3d
structure of a protein, and make modifications to the coordinates. I was
wondering if anyone can comment on suitable data structures that can be
used for this, pros and cons?

Thanks in advance!

-Sujita

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Data Structure for protein

2009-06-06T22:57:35Z

Hi,
I'm writing a program which has to hold information about the 3d
structure of a protein, and make modifications to the coordinates. I was
wondering if anyone can comment on suitable data structures that can be
used for this, pros and cons?

Thanks in advance!

-Sujita

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NETTAB 2009: Last Call for Participation

2009-05-27T09:13:36Z

Last Call for Participation

NETTAB 2009 Workshop on
"Technologies, Tools and Applications for
Collaborative and Social Bioinformatics Research and Development"
with a Special Session on:
"Methods and Tools for RNA Structure and Functional Analysis"

June 10-13, 2009
Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/

KEYNOTE TALKS

RNA WikiProject: Community annotation of RNA families
Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

Who are you? Managing collaborative digital
identities in bioinformatics with myExperiment
Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK.

Semantically Integrated eCommunities in
Biomedicine: Next-Generation Models of Biomedical Communication
Tim Clark, Director of Informatics, MassGeneral
Institute for Neurodegenerative Disease Neurology
Research Department, Massachusetts General Hospital, Boston, USA.

Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World
Gabriel Valiente, Technical University of
Catalonia, Department of Software, Barcelona, Spain.

Non coding RNAs (title to be confirmed)
Doron Betel, MSKCC - Computational Biology Center, New York, USA .

SELECTED ORAL COMMUNICATIONS

The DC-THERA Directory: A Knowledge Management
System to Support Collaboration on Dendritic Cell and Immunology Research
Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani

Bioinformatics Experimentation in a New
Agent-Based Infrastructure OpenKnowledge
Dietlind Gerloff, Xueping Quan, Adrian de
Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson

Abstraction based cooperation for the design of bioinformatics workflows
Frédéric Cadier and Philippe Picouet

Biomedical applications in the EELA-2 Project
Leandro N Ciuffo and Rafael Mayo

Make Histri: collaborative curation of exchange
histories of bacterial and archaeal type strains
Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt

SBMM Assistant: Social Pathway Annotation
Ismael Navas-Delgado, Alejandro del
Real-Chicharro, Francisca Sánchez-Jiménez and Jose F Aldana Montes

GePh-CARD: an information exchange application
for an Hub & Spoke Network for Skeletal Dysplasias
Marina Mordenti and Luca Sangiorgi

ProDaMa-C: a collaborative web application to
generate specialized protein structure datasets
Giuliano Armano and Andrea Manconi

RNA tertiary structure prediction with ModeRNA
Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki

Improved heuristic for pairwise RNA secondary structure prediction
Olivier Perriquet and Pedro Barahona

Analysing the microRNA-17-92/Myc/E2F/RB Compound
Toggle Switch by Theorem Proving
Giampaolo Bella and Pietro Liò

Mapping miRNA genes on human fragile sites and translocation breakpoints
Alfredo Ferro, rosalba giugno, Alessandro Laganà,
Alfredo Pulvirenti and Francesco Russo

MicroRNA.gr: A suite of web based tools for elucidating microRNA function
Giorgio L. Papadopoulos, Panagiotis Alexiou,
Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou

miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs
Alfredo Ferro, rosalba giugno, Alessandro Laganà,
Misael Mongiovì, Giuseppe Pigola, Alfredo
Pulvirenti, Gary Bader and Dennis Shasha

POSTERS

A web site supporting collaborative activities
within the Italian Network for Oncology Bioinformatics
Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano

Prediction of human targets for viral encoded microRNAs
Alessandro Laganà, Stefano Forte, Rosalba Giugno,
Alfredo Pulvirenti and Alfredo Ferro

Genome-wide microRNA target gene identification
and annotation using multiple prediction algorithms
Dario Corrada, Luciano Milanesi and Daniele Catalucci

Design of highly specific synthetic miRNAs
Alessandro Laganà, Stefano Forte, Angela Papa,
Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro

NETTAB '09 - Ninth International Workshop on
Network Tools and Applications in Biology
10-13 June 2009, Catania, Italy
http://www.nettab.org/2009/

Paolo Romano (paolo.romano@...)
Bioinformatics
National Cancer Research Institute (IST)

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gene expression study

2009-05-15T04:00:05Z

Hi all,
I am interested to study the expression of a set of genes from rice
and arabidopsis.Can any one tell me the simplest server/site to
perform this analysis for me.
regards
chunnu

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