Cbcb - User contributions [en]

Cbcb:Pop-Lab

2009-04-06T14:01:18Z

Niranjan: /* Progress Reports */

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]
* Metagenomics papers: [[Cbcb:Pop-Lab:Papers]]
* AMOS todos - for the summer: [[Cbcb:Pop-Lab:TODO]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Ben-Report|Ben]]
* [[Cbcb:Pop-Lab:Chris-Report|Chris]]
* [[Cbcb:Pop-Lab:James-Report|James]]
* [[Cbcb:Pop-Lab:Serge-Report|Serge]]
* [[Cbcb:Pop-Lab:Bo-Report|Bo]]
* [[Cbcb:Pop-Lab:Dan-Report|Dan]]
* [[Cbcb:Pop-Lab:Mohammad-Report|Mohammad]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Cbcb:Pop-Lab:Niranjan-Report

2009-04-06T14:00:48Z

Niranjan: /* March 2nd, 2009 */

Cbcb:Pop-Lab:Papers

2009-02-17T19:41:17Z

Niranjan: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].

Cbcb:Pop-Lab:Papers

2009-02-17T19:40:54Z

Niranjan: /* Metagenomics Reviews */

== Metagenomics Reviews ==

# V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557|A Bioinformatician's guide to Metagenomics].

Cbcb:Pop-Lab:Papers

2009-02-17T19:37:01Z

Niranjan:

== Metagenomics Reviews ==

Cbcb:Pop-Lab

2009-02-17T19:30:01Z

Niranjan: /* Important pages */

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]
* Metagenomics papers: [[Cbcb:Pop-Lab:Papers]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Ben-Report|Ben]]
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]
* [[Cbcb:Pop-Lab:Chris-Report|Chris]]
* [[Cbcb:Pop-Lab:James-Report|James]]
* [[Cbcb:Pop-Lab:Serge-Report|Serge]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Main Page

2009-02-16T15:23:33Z

Niranjan: /* People */

== Seminars ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] 
* [[Cbcb:Works-In-Progress]] - Works in progress seminar schedule (Summer 2008) 
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Kingsford-Group|Kingsford Group]]

== People ==

* [[User:pknut777|Adam Lee Bazinet]]
* [[User:amp|Adam M Phillipy]]
* [[User:adelcher|Arthur L. Delcher]]
* [[User:carlk|Carl Kinsford]]
* [[User:dpuiu|Daniela Puiu]]
* [[User:dsommer|Dan Sommer]]
* [[User:gpertea|Geo Pertea]]
* [[User:jeallen|Jonathan Edward All]]
* [[User:ayanbule|Kunmi Ayanbule]]
* [[User:conte|Matthew Conte]]
* [[User:mschatz|Michael Schatz]]
* [[User:mpertea|Mihaela Pertea]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]
* [[User:nedwards|Nathan Edwards]]
* [[User:niranjan|Niranjan Nagarajan]]
* [[User:saket|Saket Navlakha]]
* [[User:angiuoli|Samuel V Angluoli]]
* [[User:salzberg|Steven Salzberg]]
* [[User:whitej|James Robert White]]

== Getting started ==
* [[Cbcb:Resources]] (VERY) Useful information on CBCB resources 

* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:22:11Z

Niranjan: /* Papers Read */

==March 2nd, 2009==

===Tasks===

# Made more updates to my webpage
# Started making a presentation for my job talk
# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

===Papers Read===

# [[Media:rabadan2007.pdf|Non-random reassortment in human influenza A viruses]]. R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others), then given two non-reassorted strains, the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method - just a list of results which seem to clearly miss the
reassortments we already know of. In fact, in the abstract, they make the
claim that they find all the reassortments from earlier works.

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:19:16Z

Niranjan: /* Papers Read */

==March 2nd, 2009==

===Tasks===

# Made more updates to my webpage
# Started making a presentation for my job talk
# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

===Papers Read===

# [[Media:rabadan2007.pdf|Non-random reassortment in human influenza A viruses]]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:18:51Z

Niranjan: /* Papers Read */

==March 2nd, 2009==

===Tasks===

# Made more updates to my webpage
# Started making a presentation for my job talk
# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

===Papers Read===

# [Media:rabadan2007.pdf|Non-random reassortment in human influenza A viruses]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

File:Rabadan2007.pdf

2009-02-16T15:18:23Z

Niranjan: Non-random reassortment in human influenza A viruses

Non-random reassortment in human influenza A viruses

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:17:02Z

Niranjan: /* Papers Read */

==March 2nd, 2009==

===Tasks===

# Made more updates to my webpage
# Started making a presentation for my job talk
# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

===Papers Read===

# [rabadan2007.pdf| Non-random reassortment in human influenza A viruses]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:14:56Z

Niranjan:

==March 2nd, 2009==

===Tasks===

# Made more updates to my webpage
# Started making a presentation for my job talk
# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

===Papers Read===

# [http://www3.interscience.wiley.com/cgi-bin/fulltext/119423402/PDFSTART|Non-random reassortment in human influenza A viruses]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:08:36Z

Niranjan:

Report for March 2nd, 2009

[[Tasks]]

1) Made more updates to my webpage

2) Started making a presentation for my job talk

3) Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

[[Papers Read]]

1. [Non-random reassortment in human influenza A viruses]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

Cbcb:Pop-Lab:Niranjan-Report

2009-02-16T15:07:43Z

Niranjan:

Report for March 2nd, 2009

[[Tasks]]

1) Made more updates to my webpage
2) Started making a presentation for my job talk
3) Assisted Carl in writing a grant proposal to extend on our
work on reassortments in the Flu genome.

[[Papers Read]]

1. [Non-random reassortment in human influenza A viruses]
R. Rabadan, A.J. Levine and M. Krasnitz.

The basic idea in this paper is that if you assume constant
rate of mutational drift in different segments of the same strain (an
assumption that seems to be true on a coarse level for some segments, but
not for others) then given two non-reassorted strains the nucleotide
differences between their NA segments should be roughly proportional to
that from the HA segments and they use that as a test to identify putative
reassortments. They use a vaguely described idea to figure out which
combination of segments have reassorted (probably done manually) and they
seem to make no attempt to figure out if a set of taxa have reassorted
based on a common event. Finally, there is no evaluation of the capability
of this method, just a list of results which seem to clearly miss the
reassortments we already know of! In fact they make the claim that they
find all the reassortments from earlier works, in the abstract!

Cbcb:Pop-Lab

2009-02-11T20:26:00Z

Niranjan:

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Cbcb:Pop-Lab:Niranjan-Report

2009-02-11T20:24:22Z

Niranjan:

Report for March 2nd, 2009

Cbcb:Pop-Lab

2009-02-11T20:22:59Z

Niranjan:

= Important pages =
* Group members [[Cbcb:Pop-Lab:Members]]
* Blog: [http://genomes.blogspot.com Genomes.blogspot.com]
* How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.
* Software developed by us: [[Cbcb:Pop-Lab:Software]]

= Meetings/seminars =
* [[Pop_group_meeting|Group meeting]]: every Monday from 3pm in corner conference room (3120 C)
* Group meeting: every Thursday 3-4pm in corner conference room (3120 C)
* CBCB works-in-progress seminar: Mondays 1:30-2:30pm during the summer in main conference room
* [http://www.cbcb.umd.edu/seminars CBCB seminar ]: Thursdays 2-3pm during the semester in main conference room
* [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room

= Progress Reports =
* [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]

= Pop Lab Presentations =
* [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]]
* Listeria Monocytogenes Slides (powerpoint)
* Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]

Pop group meeting

2008-10-20T20:59:40Z

Niranjan: /* 10/13/2008 */

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology

= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
# Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database
create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

= 10/20/2008 =
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008

Pop group meeting

2008-10-20T20:57:56Z

Niranjan: /* 10/13/2008 */

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology

= 10/13/2008 =
# Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database # create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

# Bo Liu & James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

= 10/20/2008 =
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008

Pop group meeting

2008-10-20T20:57:11Z

Niranjan: /* 09/29/2008 */

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology

= 10/13/2008 =
# Daniela Puiu (Daniel Sommer, same paper) [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database # create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

# Bo Liu & James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

= 10/20/2008 =
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008

Pop group meeting

2008-10-20T20:55:47Z

Niranjan: /* 10/20/2008 */

= 09/29/2008 =

# Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)
# Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)
# Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)
# Dan Sommer [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V73-4SHVST0-1&_user=961305&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=961305&md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)
# Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)
# Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)
# Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)
# Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)

= 10/06/2008 =
# Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS
# Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics
# James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS
# MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology

= 10/13/2008 =
# Daniela Puiu (Daniel Sommer, same paper) [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE
MetaSim software:
Location: /fs/sz-user-supported/common/packages/MetaSim/
Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim
Database: /fs/sz-user-supported/common/packages/MetaSim/database # create a symlink to it from your working directory, otherwise you have to import it
NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]

# Bo Liu & James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science
# MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)

= 10/20/2008 =
# Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR
# Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology
# Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008

Cbcb:Works-In-Progress

2008-09-04T20:48:31Z

Niranjan: /* CBCB Works in Progress seminars */

== CBCB Works in Progress seminars ==
'''When:''' Mondays @ 1:30pm 
'''Where:''' Main CBCB conference room 
 

'''Schedule''' 
{|
|6/9 || Mike Schatz || slides
|-
|6/16 || Cole Trapnell || slides
|-
|6/23 || Ben Langmead || slides
|-
|6/30 || Sam Huang || slides
|-
|7/14 || Adam Phillippy || slides
|-
|7/21 || Ginger Houston-Ludlam || slides
|-
|-
|7/28 || Canceled || slides
|-
|-
|8/4 || Saket Navlakha || slides
|-
|8/11 || ''Canceled'' || slides
|-
|8/18 || Bo Liu || slides
|-
|8/25 || Gustavo Cerqueira || slides
|-
|}

Cbcb:Pop-Lab:How-to

2008-09-04T20:14:20Z

Niranjan: /* How-To repository */

==How-To repository==
[http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] 
[[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] 
[[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] 
How do I annotate a genome at the CBCB? 
How do I run the new Bambus? 
How do I use the antibiotic resistance database? 
How do I use the antibiotic resistance database locally? 
How do I run jobs on the grid? 
How do I compare metagenomic datasets through the metastats website? 
How do I compare metagenomic datasets using R directly? 
How do I find CRISPRs in a new genome? 
[[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] 
How do I generate graph information out of Minimus? 
What tools are available for doing in silico finishing at the CBCB? 
How do I generate a scaffold graph starting from a 454 .ace file? 
How do I draw a pretty picture of a scaffold stored in an AMOS bank?

Cbcb:Works-In-Progress

2008-07-08T17:08:31Z

Niranjan: /* CBCB Works in Progress seminars */

== CBCB Works in Progress seminars ==
'''When:''' Mondays @ 1:30pm 
'''Where:''' Main CBCB conference room 
 

'''Schedule''' 
{|
|6/9 || Mike Schatz || slides
|-
|6/16 || Cole Trapnell || slides
|-
|6/23 || Ben Langmead || slides
|-
|6/30 || Sam Huang || slides
|-
|7/14 || Adam Phillippy || slides
|-
|7/21 || Ginger Houston-Ludlam || slides
|-
|7/28 || Daniel Sommer || slides
|-
|8/4 || Saket Navlakha || slides
|-
|8/11 || Sam Angiouoli || slides
|-
|8/18 || Bo Liu || slides
|-
|8/25 || Gustavo Cerqueira || slides
|-
|9/8 || Niranjan Nagarajan || slides
|-
|}

Cbcb:Works-In-Progress

2008-06-16T17:26:07Z

Niranjan: /* CBCB Works in Progress seminars */

== CBCB Works in Progress seminars ==
'''When:''' Mondays @ 1:30pm 
'''Where:''' Main CBCB conference room 
 

'''Schedule''' 
{|
|6/9 || Mike Schatz || slides
|-
|6/16 || Cole Trapnell || slides
|-
|6/23 || Ben Langmead || slides
|-
|6/30 || Sam Huang || slides
|-
|7/7 || Dan Sommer || slides
|-
|7/14 || Adam Phillippy || slides
|-
|7/21 || Ginger Houston-Ludlam || slides
|-
|7/28 || Niranjan Nagarajan || slides
|-
|8/4 || Saket Navlakha || slides
|-
|8/11 || Sam Angiouoli || slides
|-
|8/18 || Bo Liu || slides
|-
|8/25 || Gustavo Cerqueira || slides
|}