Cbcb - User contributions [en]

Cbcb:Pop-Lab

2011-06-28T18:46:50Z

Jpaulson: /* Tutorials/Documenation */

= 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]]
* TODO items (please volunteer to take some of these on): [[Cbcb:Pop-Lab:TODO]]
* Grand Challenges: [[Cbcb:Pop-Lab:Challenges]] - research challenges

= Tutorials/Documenation =
BWT 2011 (Bioinformatics Whirwind Tour 2011)
Format: 1 hour lectures, informal, theory + tools.
''June 27th - July 1st''

* [http://cbcb.umd.edu/data/assembly_lecture.pptx Intro to NGS Genome Assembly] (Sergey & Todd, Monday @ 12:30pm)
* [http://cbcb.umd.edu/data/stats_intern.pptx Intro to Statistics] (Joe, Tuesday @ noon )
* Intro to Sequence Alignment (Mohammad & Todd, Wednesday @ 4pm)
* Intro to Gene/motif/pattern finding (Dan & Bo, Thursday @ 1:30pm)
* Intro to Clustering (Irina, Friday @ )

= 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
* [[Summer_Reading_Group_2009|Summer Reading Group 2009 (Computational Metabolic Pathway Analysis)]]: Fridays from 2ish-5ish in 3120C in the SE corner of the Bioscience Research Building (BSB) from June 5-August 28

= 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]]
* [[Cbcb:Pop-Lab:Ted-Report|Ted]]

= 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

2011-06-28T18:37:20Z

Jpaulson: /* Tutorials/Documenation */

= 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]]
* TODO items (please volunteer to take some of these on): [[Cbcb:Pop-Lab:TODO]]
* Grand Challenges: [[Cbcb:Pop-Lab:Challenges]] - research challenges

= Tutorials/Documenation =
BWT 2011 (Bioinformatics Whirwind Tour 2011)
Format: 1 hour lectures, informal, theory + tools.
''June 27th - July 1st''

* [http://cbcb.umd.edu/data/assembly_lecture.pptx Intro to NGS Genome Assembly] (Sergey & Todd, Monday @ 12:30pm)
* [http://cbcb.umd.edu/data/stats_inter.pptx] Intro to Statistics (Joe, Tuesday @ noon )
* Intro to Sequence Alignment (Mohammad & Todd, Wednesday @ 4pm)
* Intro to Gene/motif/pattern finding (Dan & Bo, Thursday @ 1:30pm)
* Intro to Clustering (Irina, Friday @ )

= 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
* [[Summer_Reading_Group_2009|Summer Reading Group 2009 (Computational Metabolic Pathway Analysis)]]: Fridays from 2ish-5ish in 3120C in the SE corner of the Bioscience Research Building (BSB) from June 5-August 28

= 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]]
* [[Cbcb:Pop-Lab:Ted-Report|Ted]]

= 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)]]

User:Jpaulson

2010-07-08T02:41:15Z

Jpaulson:

Joseph N. Paulson: PhD student in Applied Mathematics, Scientific Computation

Google voice # (301) 246-0336

User:Jpaulson

2010-07-08T02:40:25Z

Jpaulson:

Joseph N. Paulson: PhD student in Applied Mathematics, Scientific Computation

User:Jpaulson

2010-07-08T02:40:12Z

Jpaulson:

Joseph N. Paulson PhD student in Applied Mathematics, Scientific Computation

Main Page

2010-07-08T02:39:28Z

Jpaulson: /* People */

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

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Kingsford-Group|Kingsford Group]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam 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:mschatz|Michael Schatz]]
* [[User:jpaulson|Joseph Paulson]]
* [[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:tgibbons | Ted Gibbons]]
* [[User:whitej|James Robert White]]

== Getting started ==
If you have just received a new umiacs account through CBCB, follow the instructions on this page to get the basic information you'll need to start working:<br>
*[[Getting Started in CBCB]]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB Computers]
*[[Communal Software]]