Difference between revisions of "2009 GMOD Summer School - Americas"
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{| style="vertical-align: middle; border: 2px solid #A6A6BC" cellpadding="10" | {| style="vertical-align: middle; border: 2px solid #A6A6BC" cellpadding="10" | ||
− | | [[ | + | | [[File:2009SummerSchoolAmericas300.png|center]] |
| <span style="font-size: 200%; line-height: 120%"><b>2009 GMOD Summer School - Americas</b><br />16-19 July, 2009<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span> | | <span style="font-size: 200%; line-height: 120%"><b>2009 GMOD Summer School - Americas</b><br />16-19 July, 2009<br />[http://www.nescent.org/ NESCent]<br />Durham, NC, USA</span> | ||
|} | |} | ||
</center> | </center> | ||
− | |||
− | The '''''2009 GMOD Summer School - Americas''''' | + | The '''''2009 GMOD Summer School - Americas''''' was held 16-19 July at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina. Like the [[2008 GMOD Summer School]], this course focused on installing, configuring and integrating popular [[GMOD Components]]. |
− | + | The course wiki is [https://www.nescent.org/courses/2009/gmod/Americas here] (login required). | |
− | == | + | Another [[GMOD Summer School]] was offered in [[2009 GMOD Summer School - Europe|Oxford, UK in August, 2009]], as part of [[GMOD Europe 2009]]. |
+ | |||
+ | == Program == | ||
+ | |||
+ | The program featured 4 full days of hands-on training starting with an overview of GMOD, and then covering the installation, configuration, and administration of several popular [[GMOD Components]]. | ||
+ | <div class="emphasisbox"> | ||
+ | The summer school GMOD component sessions are available as [[Training and Outreach#Online Tutorials|online tutorials]]. To access the tutorials, follow the links for [[MAKER Tutorial|MAKER]], [[JBrowse Tutorial|JBrowse]], [[Chado Tutorial|Chado]], [[Apollo Tutorial|Apollo]], [[GBrowse Tutorial|GBrowse]], [[BioMart Tutorial|BioMart]], [[GBrowse_syn Tutorial|GBrowse_syn]], and [[Tripal Tutorial|Tripal]] | ||
+ | </div> | ||
− | |||
{| class="wikitable" border="1" cellpadding="5" cellspacing="0" | {| class="wikitable" border="1" cellpadding="5" cellspacing="0" | ||
|- | |- | ||
− | |||
! width="7%" style="background-color: #99ccff" | Time | ! width="7%" style="background-color: #99ccff" | Time | ||
− | ! width=" | + | ! width="93%" style="background-color: #99ccff" | Session |
|- | |- | ||
− | | colspan=" | + | | colspan="2" | |
|- | |- | ||
− | ! | + | ! colspan="2" style="background-color: #bbffff" | Thursday<br />July 16 |
+ | |- | ||
! style="background-color: #ccffff" | 8:45am | ! style="background-color: #ccffff" | 8:45am | ||
| style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview | | style="background-color: #ddffff" align="center" | '''Introduction and Overview'''<br />[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]<br />Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview | ||
|- | |- | ||
! style="background-color: #ccffff" | 10:25am | ! style="background-color: #ccffff" | 10:25am | ||
− | | style="background-color: #ddffff" align="center" | '''VMware and BioPerl Setup'''<br />'''Everyone'''<br />Get the GMOD Summer School [[#System Requirements|VMware]] image up and running on your laptop, and then finish installation of [[BioPerl]]. | + | | style="background-color: #ddffff" align="center" | '''[[VMware]] and [[BioPerl]] Setup'''<br />'''Everyone'''<br />Get the GMOD Summer School [[#System Requirements|VMware]] image up and running on your laptop, and then finish installation of [[BioPerl]]. |
|- | |- | ||
! style="background-color: #ccffff" | 12:15pm | ! style="background-color: #ccffff" | 12:15pm | ||
− | | style="background-color: #ddffff" align="center" | '''Lunch''' | + | | style="background-color: #ddffff" align="center" | '''Lunch'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ccffff" | 1:15pm | ! style="background-color: #ccffff" | 1:15pm | ||
− | | style="background-color: #ddffff" align="center" | '''[[MAKER]] | + | | style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER I]]'''<br />[[User:Carsonholt|Carson Holt]]<br />[[MAKER]] overview, installation, and basic configuration for annotating genomic sequence |
|- | |- | ||
! style="background-color: #ccffff" | 4:30pm | ! style="background-color: #ccffff" | 4:30pm | ||
− | | style="background-color: #ddffff" align="center" | '''Social Hour w/ [http://www.nescent.org/dir/ NESCent Staff]<br />and then Dinner''' | + | | style="background-color: #ddffff" align="center" | '''Social Hour w/ [http://www.nescent.org/dir/ NESCent Staff]'''<br />and then '''Dinner''' [http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ccffff" | 6:30pm | ! style="background-color: #ccffff" | 6:30pm | ||
− | | style="background-color: #ddffff" align="center" | '''[[MAKER]] | + | | style="background-color: #ddffff" align="center" | '''[[MAKER Tutorial|MAKER II]]'''<br />[[User:Carsonholt|Carson Holt]]<br />Advanced [[MAKER]] configuration, re-annotation options, and improving annotation quality |
|- | |- | ||
! style="background-color: #ccffff" | 7:30pm | ! style="background-color: #ccffff" | 7:30pm | ||
− | | style="background-color: #ddffff" align="center" | '''[[JBrowse]]'''<br />[[User: | + | | style="background-color: #ddffff" align="center" | '''[[JBrowse Tutorial|JBrowse]]'''<br />[[User:MitchSkinner|Mitch Skinner]]<br />[[JBrowse]] installation, configuration and administration; converting [[GFF3]] to [[Glossary#JSON|JSON]] and loading it into JBrowse. |
|- | |- | ||
! style="background-color: #ccffff" | 9:00pm | ! style="background-color: #ccffff" | 9:00pm | ||
| style="background-color: #ddffff" align="center" | Day ends | | style="background-color: #ddffff" align="center" | Day ends | ||
|- | |- | ||
− | | colspan=" | + | | colspan="2" | |
+ | |- | ||
+ | ! colspan="2" style="background-color: #bbffcc"| Friday<br />July 17 | ||
|- | |- | ||
− | |||
! style="background-color: #ccffdd" | 8:45am | ! style="background-color: #ccffdd" | 8:45am | ||
− | | style="background-color: #ddffdd" align="center" | '''[[ | + | | style="background-color: #ddffdd" align="center" | '''[[Chado Tutorial|Chado I]]'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]] |
|- | |- | ||
! style="background-color: #ccffdd" | 12:30pm | ! style="background-color: #ccffdd" | 12:30pm | ||
− | | style="background-color: #ddffdd" align="center" | '''Lunch''' | + | | style="background-color: #ddffdd" align="center" | '''Lunch'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ccffdd" | 1:30pm | ! style="background-color: #ccffdd" | 1:30pm | ||
− | | style="background-color: #ddffdd" align="center" | '''[[ | + | | style="background-color: #ddffdd" align="center" | '''[[Chado Tutorial|Chado II]]'''<br />[[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]] |
|- | |- | ||
! style="background-color: #ccffdd" | 3:00pm | ! style="background-color: #ccffdd" | 3:00pm | ||
− | | style="background-color: #ddffdd" align="center" | '''[[Apollo]] | + | | style="background-color: #ddffdd" align="center" | '''[[Apollo Tutorial|Apollo I]]'''<br />[[User:Elee|Ed Lee]]<br />Overview, basic installation, basic configuration, reading/writing data, and remote analyses. |
|- | |- | ||
! style="background-color: #ccffdd" | 5:30pm | ! style="background-color: #ccffdd" | 5:30pm | ||
− | | style="background-color: #ddffdd" align="center" | '''Dinner''' | + | | style="background-color: #ddffdd" align="center" | '''Dinner'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ccffdd" | 7:00pm | ! style="background-color: #ccffdd" | 7:00pm | ||
− | | style="background-color: #ddffdd" align="center" | '''[[Apollo]] | + | | style="background-color: #ddffdd" align="center" | '''[[Apollo Tutorial|Apollo II]]'''<br />[[User:Elee|Ed Lee]]<br />Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance. |
|- | |- | ||
! style="background-color: #ccffdd" | 9:00pm | ! style="background-color: #ccffdd" | 9:00pm | ||
| style="background-color: #ddffdd" align="center" | Day ends | | style="background-color: #ddffdd" align="center" | Day ends | ||
|- | |- | ||
− | | colspan=" | + | | colspan="2" | |
+ | |- | ||
+ | ! colspan="2" style="background-color: #ffffaa" | Saturday<br />July 18 | ||
|- | |- | ||
− | |||
! style="background-color: #ffffbb" | 8:45am | ! style="background-color: #ffffbb" | 8:45am | ||
− | | style="background-color: #ffffcc" align="center" |'''[[ | + | | style="background-color: #ffffcc" align="center" |'''[[GBrowse Tutorial|GBrowse I]]'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]<br /> |
|- | |- | ||
! style="background-color: #ffffbb" | 12:30pm | ! style="background-color: #ffffbb" | 12:30pm | ||
− | | style="background-color: #ffffcc" align="center" |'''Lunch''' | + | | style="background-color: #ffffcc" align="center" |'''Lunch'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ffffbb" | 1:30pm | ! style="background-color: #ffffbb" | 1:30pm | ||
− | | style="background-color: #ffffcc" align="center" |'''[[ | + | | style="background-color: #ffffcc" align="center" |'''[[GBrowse Tutorial|GBrowse II]]'''<br />[[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]] |
|- | |- | ||
! style="background-color: #ffffbb" | 2:30pm | ! style="background-color: #ffffbb" | 2:30pm | ||
− | | style="background-color: #ffffcc" align="center" |'''[[BioMart]] | + | | style="background-color: #ffffcc" align="center" |'''[[BioMart Tutorial|BioMart]]'''<br />[[User:Junjun|Junjun Zhang]]<br />Introduction; exploring over 20 public databases through [[BioMart]] central portal; system installation; accessing BioMart server via API, webservice and [[DAS]]; configuration of BioMart server including federation; demonstration of creating data mart. |
|- | |- | ||
− | ! style="background-color: #ffffbb" | | + | ! style="background-color: #ffffbb" | 6:00pm |
− | | style="background-color: #ffffcc" align="center" |'''Dinner''' | + | | style="background-color: #ffffcc" align="center" |'''Dinner'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
− | ! style="background-color: #ffffbb" | 7: | + | ! style="background-color: #ffffbb" | 7:30pm |
− | | style="background-color: #ffffcc" align="center" |''' | + | | style="background-color: #ffffcc" align="center" |'''Open Discussion''' and '''User Presentations'''<br />Everyone<br />This ''optional'' session is open to any and all questions you have on the [[Main Page|GMOD Project]], [[GMOD Components]], and GMOD users. The instructors will come with their knowledge of GMOD and their opinions on the project's strengths, weaknesses, and future directions. Students will also have the opportunity to share work from their projects with the rest of the group. |
+ | We expect this session to be ''lively''. | ||
|- | |- | ||
! style="background-color: #ffffbb" | 9:00pm | ! style="background-color: #ffffbb" | 9:00pm | ||
| style="background-color: #ffffcc" align="center" |Day ends | | style="background-color: #ffffcc" align="center" |Day ends | ||
|- | |- | ||
− | | colspan=" | + | | colspan=2" | |
+ | |- | ||
+ | ! colspan="2" style="background-color: #ffccaa" | Sunday<br />July 19 | ||
|- | |- | ||
− | |||
! style="background-color: #ffddcc" | 8:45am | ! style="background-color: #ffddcc" | 8:45am | ||
− | | style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn]]'''<br />[[User:Mckays|Sheldon | + | | style="background-color: #ffeedd" align="center" |'''[[GBrowse_syn Tutorial|GBrowse_syn]]'''<br />[[User:Mckays|Sheldon McKay]] |
|- | |- | ||
! style="background-color: #ffddcc" | 12:30pm | ! style="background-color: #ffddcc" | 12:30pm | ||
− | | style="background-color: #ffeedd" align="center" |'''Lunch''' | + | | style="background-color: #ffeedd" align="center" |'''Lunch'''<br />[http://www.ninthst.com/ on your own] |
|- | |- | ||
! style="background-color: #ffddcc" | 1:30pm | ! style="background-color: #ffddcc" | 1:30pm | ||
− | | style="background-color: #ffeedd" align="center" |'''[[ | + | | style="background-color: #ffeedd" align="center" |'''[[Tripal Tutorial|Tripal]]'''<br />[[User:sficklin|Stephen Ficklin]]<br />[[Tripal]] is a web front end to [[Chado]] databases built on [http://www.drupal.org/ Drupal]. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration. |
|- | |- | ||
! style="background-color: #ffddcc" | 6:00pm | ! style="background-color: #ffddcc" | 6:00pm | ||
Line 115: | Line 124: | ||
|} | |} | ||
− | == | + | == Instructors == |
− | + | <center> | |
{| class="wikitable" | {| class="wikitable" | ||
! Instructor | ! Instructor | ||
− | ! GMOD | + | ! GMOD Affiliation |
! Affiliation | ! Affiliation | ||
|- | |- | ||
| [[User:Scott|Scott Cain]] | | [[User:Scott|Scott Cain]] | ||
− | | GMOD Project Coordinator | + | | GMOD Project Coordinator; [[Chado]] develoepr |
| [http://www.oicr.on.ca/ Ontario Institute for Cancer Research] | | [http://www.oicr.on.ca/ Ontario Institute for Cancer Research] | ||
|- | |- | ||
Line 130: | Line 139: | ||
| [http://nescent.org/ National Evolutionary Synthesis Center (NESCent)] | | [http://nescent.org/ National Evolutionary Synthesis Center (NESCent)] | ||
|- | |- | ||
− | | Stephen Ficklin | + | | [[User:sficklin|Stephen Ficklin]] |
− | | | + | | [[Tripal]] developer |
| [http://www.genome.clemson.edu/ Clemson University Genomics Institute] | | [http://www.genome.clemson.edu/ Clemson University Genomics Institute] | ||
|- | |- | ||
− | | Ed Lee | + | | [[User:Carsonholt|Carson Holt]] |
− | | | + | | [[MAKER]] developer |
+ | | [http://www.utah.edu University of Utah] | ||
+ | |- | ||
+ | | [[User:Elee|Ed Lee]] | ||
+ | | [[Apollo]] developer | ||
| [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)] | | [http://www.berkeleybop.org/ Berkeley Bioinformatics Open-source Projects (BBOP)] | ||
|- | |- | ||
− | | [[User:Mckays|Sheldon | + | | [[User:Mckays|Sheldon McKay]] |
− | | | + | | [[GBrowse_syn]] developer, [[GBrowse]] developer |
| [http://cshl.edu Cold Spring Harbor Laboratory] | | [http://cshl.edu Cold Spring Harbor Laboratory] | ||
|- | |- | ||
− | | Joshua Orvis | + | | [[User:Jorvis|Joshua Orvis]] |
− | | | + | | [[Ergatis]] developer and power [[Chado]] user |
| [http://www.igs.umaryland.edu/ Institute for Genome Sciences] | | [http://www.igs.umaryland.edu/ Institute for Genome Sciences] | ||
|- | |- | ||
− | | | + | | [[User:MitchSkinner|Mitch Skinner]] |
− | | [[ | + | | [[JBrowse]] developer |
− | | [http:// | + | | [http://berkeley.edu University of California, Berkeley] |
|- | |- | ||
− | | Junjun Zhang | + | | [[User:Junjun|Junjun Zhang]] |
| [[BioMart]] developer | | [[BioMart]] developer | ||
| [http://www.oicr.on.ca/ Ontario Institute for Cancer Research] | | [http://www.oicr.on.ca/ Ontario Institute for Cancer Research] | ||
|} | |} | ||
+ | </center> | ||
== Prerequisites == | == Prerequisites == | ||
Line 162: | Line 176: | ||
{| | {| | ||
− | | | + | | [[File:VmwareLogoSmall.jpg|link=http://www.vmware.com|VMware]] |
− | |''Participants are required to bring their own laptops, already capable of running a [ | + | |''Participants are required to bring their own laptops, already capable of running a [[VMware]] system image.'' |
|} | |} | ||
− | The course | + | The course started with getting a [ftp://ftp.gmod.org/pub/gmod/Courses/2009/SummerSchoolAmericas/GmodSumSch2009Amer1.zip VMware image built specifically for the course] up and running on your machine. We then built upon that image in each succeeding session. |
− | {{2009SummerSchoolSystemOptions}} | + | {{2009SummerSchoolSystemOptions|$80}} |
− | == | + | == Cost == |
− | + | This course was ''free'' thanks to [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=7234938&p_grant_num=1R01HG004483-01&p_query=&ticket=&p_audit_session_id=&p_keywords= NIH grant 1R01HG004483-01] under [http://biowiki.org/IanHolmes Ian Holmes], and to the grants of the individual instructors. | |
− | == | + | == Feedback == |
− | + | 17 of 25 students provided feedback on the course. | |
− | |||
− | + | '''Q: Would you recommend [[GMOD Summer School]] to others?''' | |
+ | {| class="wikitable" | ||
+ | ! No | ||
+ | ! Yes, with reservations | ||
+ | ! Yes | ||
+ | ! No opinion | ||
+ | |- | ||
+ | | 0% | ||
+ | | 12% | ||
+ | ! 88% | ||
+ | | 0% | ||
+ | |} | ||
− | |||
− | + | '''Q: Please rate the quality of the sessions overall, from 1 (very poor) to 3 (average) to 5 (very good), or N.A. if you have no opinion.''' | |
+ | |||
+ | {| class="wikitable" | ||
+ | ! Very Poor<br />1 | ||
+ | ! (Poor)<br />2 | ||
+ | ! Average<br />3 | ||
+ | ! (Good)<br />4 | ||
+ | ! Very Good<br />5 | ||
+ | ! N.A. | ||
+ | |- | ||
+ | | 0% | ||
+ | | 0% | ||
+ | | 12% | ||
+ | ! 59% | ||
+ | | 23% | ||
+ | | 6% | ||
+ | |} | ||
+ | [[Category:Tutorials]] | ||
[[Category:Education and Outreach]] | [[Category:Education and Outreach]] | ||
+ | [[Category:Events]] | ||
+ | [[Category:GMOD Schools]] |
Latest revision as of 22:13, 16 April 2014
2009 GMOD Summer School - Americas 16-19 July, 2009 NESCent Durham, NC, USA |
The 2009 GMOD Summer School - Americas was held 16-19 July at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. Like the 2008 GMOD Summer School, this course focused on installing, configuring and integrating popular GMOD Components.
The course wiki is here (login required).
Another GMOD Summer School was offered in Oxford, UK in August, 2009, as part of GMOD Europe 2009.
Program
The program featured 4 full days of hands-on training starting with an overview of GMOD, and then covering the installation, configuration, and administration of several popular GMOD Components.
The summer school GMOD component sessions are available as online tutorials. To access the tutorials, follow the links for MAKER, JBrowse, Chado, Apollo, GBrowse, BioMart, GBrowse_syn, and Tripal
Time | Session |
---|---|
Thursday July 16 | |
8:45am | Introduction and Overview Scott Cain and Dave Clements Participant and instructor introductions, how the GMOD project works, what software tools are available in GMOD, how they interoperate, what resources are needed to get a GMOD installation up and running, and course overview |
10:25am | VMware and BioPerl Setup Everyone Get the GMOD Summer School VMware image up and running on your laptop, and then finish installation of BioPerl. |
12:15pm | Lunch on your own |
1:15pm | MAKER I Carson Holt MAKER overview, installation, and basic configuration for annotating genomic sequence |
4:30pm | Social Hour w/ NESCent Staff and then Dinner on your own |
6:30pm | MAKER II Carson Holt Advanced MAKER configuration, re-annotation options, and improving annotation quality |
7:30pm | JBrowse Mitch Skinner JBrowse installation, configuration and administration; converting GFF3 to JSON and loading it into JBrowse. |
9:00pm | Day ends |
Friday July 17 | |
8:45am | Chado I Scott Cain, Joshua Orvis, and Dave Clements |
12:30pm | Lunch on your own |
1:30pm | Chado II Scott Cain, Joshua Orvis, and Dave Clements |
3:00pm | Apollo I Ed Lee Overview, basic installation, basic configuration, reading/writing data, and remote analyses. |
5:30pm | Dinner on your own |
7:00pm | Apollo II Ed Lee Custom installation (building Apollo from source), advanced configuration, and setting up customized Java Web Start instance. |
9:00pm | Day ends |
Saturday July 18 | |
8:45am | GBrowse I Scott Cain and Sheldon McKay |
12:30pm | Lunch on your own |
1:30pm | GBrowse II Scott Cain and Sheldon McKay |
2:30pm | BioMart Junjun Zhang Introduction; exploring over 20 public databases through BioMart central portal; system installation; accessing BioMart server via API, webservice and DAS; configuration of BioMart server including federation; demonstration of creating data mart. |
6:00pm | Dinner on your own |
7:30pm | Open Discussion and User Presentations Everyone This optional session is open to any and all questions you have on the GMOD Project, GMOD Components, and GMOD users. The instructors will come with their knowledge of GMOD and their opinions on the project's strengths, weaknesses, and future directions. Students will also have the opportunity to share work from their projects with the rest of the group. We expect this session to be lively. |
9:00pm | Day ends |
Sunday July 19 | |
8:45am | GBrowse_syn Sheldon McKay |
12:30pm | Lunch on your own |
1:30pm | Tripal Stephen Ficklin Tripal is a web front end to Chado databases built on Drupal. This class will introduce Drupal and Tripal architecture, and then cover Tripal installation, configuration and administration. |
6:00pm | Wrapup and Resources Dave Clements and Scott Cain |
6:30pm | Summer School Ends |
Instructors
Instructor | GMOD Affiliation | Affiliation |
---|---|---|
Scott Cain | GMOD Project Coordinator; Chado develoepr | Ontario Institute for Cancer Research |
Dave Clements | GMOD Help Desk | National Evolutionary Synthesis Center (NESCent) |
Stephen Ficklin | Tripal developer | Clemson University Genomics Institute |
Carson Holt | MAKER developer | University of Utah |
Ed Lee | Apollo developer | Berkeley Bioinformatics Open-source Projects (BBOP) |
Sheldon McKay | GBrowse_syn developer, GBrowse developer | Cold Spring Harbor Laboratory |
Joshua Orvis | Ergatis developer and power Chado user | Institute for Genome Sciences |
Mitch Skinner | JBrowse developer | University of California, Berkeley |
Junjun Zhang | BioMart developer | Ontario Institute for Cancer Research |
Prerequisites
The course requires a minimal level of Linux systems administration knowledge (see Computing Requirements). By "a minimal level of Linux systems administration knowledge" we mean that participants should be comfortable installing packages under Linux. A good benchmark for this level of knowledge is that you should be able to get a basic GBrowse installation (that is, GBrowse without MySQL) up and running with the example GBrowse data. This also requires installing Apache, and BioPerl and all its dependencies.
Getting a basic GBrowse up and running on your system will be assigned as homework to be done prior to the course's start.
System Requirements
Participants are required to bring their own laptops, already capable of running a VMware system image. |
The course started with getting a VMware image built specifically for the course up and running on your machine. We then built upon that image in each succeeding session.
- VMware on Windows and Linux
- VMware on Mac OS X
Participants can also bring newer Macs with Intel processors. The Intel processor is a requirement for all the packages discussed below.
There is no free VMware player that runs directly under Mac OS X. However, there are several other options, all of which require an Intel Mac:
- VMware Fusion
- Mac OS 10.5 (Leopard) and Boot Camp
The Leopard release of Mac OS (10.5) includes Boot Camp, a feature that allows you to boot your Mac into another operating system, including Windows or Linux. From there you can install the VMware player for your OS.*
* Apple tells you that you can partition your disk drive at any time using Boot Camp. In practice, this appears to only work easily when you first get your system.
Cost
This course was free thanks to NIH grant 1R01HG004483-01 under Ian Holmes, and to the grants of the individual instructors.
Feedback
17 of 25 students provided feedback on the course.
Q: Would you recommend GMOD Summer School to others?
No | Yes, with reservations | Yes | No opinion |
---|---|---|---|
0% | 12% | 88% | 0% |
Q: Please rate the quality of the sessions overall, from 1 (very poor) to 3 (average) to 5 (very good), or N.A. if you have no opinion.
Very Poor 1 |
(Poor) 2 |
Average 3 |
(Good) 4 |
Very Good 5 |
N.A. |
---|---|---|---|---|---|
0% | 0% | 12% | 59% | 23% | 6% |