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- | ====== Contributors to UCSC Banana Slug Genome Assembly (BME 235) ====== | + | ======Contributors====== |
+ | A list of all people (past and present) that have worked on the project. People marked with a bold **contributor** tag are current contributors. | ||
- | We should standardize on a single image size for everyone to use (maybe 200 pixels high by 150 wide?), and also decide how we want to order the contributors (alphabetical, by type of work done, ...). This suggestion should be replaced by the decision once the class makes it. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/03/30 07:59// | + | =====2015===== |
+ | For the 2015 BME 235 class the class was split into five different teams. Each team was given an assembly program to work with throughout the quarter. | ||
- | ===== Here are a couple of Unix commands that may help you get your images in a standard format for this page. ===== | + | ===Roster=== |
+ | | Ed Green | ed@soe.ucsc.edu | Teacher | | ||
+ | | Kevin Karplus | karplus@soe.ucsc.edu| Teacher, **contributor** | | ||
+ | | Charles Cole | chkcole@ucsc.edu | Student, **contributor** | | ||
+ | | Kyle McGovern | kmcgover@ucsc.edu | Student | | ||
+ | | Jake Houser | jdhouser@ucsc.edu | Student | | ||
+ | | Jennie Richardson | jemricha@ucsc.edu | Student | | ||
+ | | Thomas Matthew| thjmatth@ucsc.edu | Student | | ||
+ | | Charles Markello | cmarkell@ucsc.edu | Student, **contributor** | | ||
+ | | Nedda Saremi | nsaremi@ucsc.edu | Student | | ||
+ | | Josh Espinoza | | Student | | ||
+ | | Christopher Kan | | Student | | ||
+ | | Audry Musselman-Brown | | Student | | ||
+ | | Jared Copher | jcopher@ucsc.edu | Student, **contributor**| | ||
+ | | Feal | efeal@ucsc.edu | Student | | ||
+ | | Sidra Hussain | sihussai@ucsc.edu | Student | | ||
+ | | Gepoliano Chaves | gchaves@ucsc.edu | Student | | ||
+ | | Natasha Dudek | natasha@dudek.org | Student, **contributor** | | ||
+ | | Robert Calef | rcalef@ucsc.edu | Student | | ||
+ | | Christopher Eisenhart | ceisenha@ucsc.edu | Student, **contributor** | | ||
+ | | Daren Liu | darenliu@berkley.edu | Past external contributor | | ||
+ | === Assembly Teams === | ||
+ | | Number | Team members | Assembler | Team page | | ||
+ | | 1 | Cole, McGovern, Houser, Richardson | [[http://jgi.doe.gov/data-and-tools/meraculous/|Meraculous]] | [[contributors:team_1_page| Team 1 ]]| | ||
+ | | 2 | Matthew, Markello, Saremi | [[http://soap.genomics.org.cn/soapdenovo.html|SOAP denovo]] | [[contributors:team_2_page| Team 2]]| | ||
+ | | 3 | Espinoza, Kan, Musselman-Brown | [[ https://github.com/jts/sga|SGA]] | [[contributors:team_3_page| Team 3]] | | ||
+ | | 4 | Copher, Feal, Hussain | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] | [[contributors:team_4_page| Team 4 ]]| | ||
+ | | 5 | Chaves, Calef, Dudek, Eisenhart | [[ http://www.broadinstitute.org/software/discovar/blog/|Discovar denovo]] | [[contributors:team_5_page| Team 5 ]]| | ||
- | To rotate files in unix 90 degrees clockwise you can use **jpegtran**. | + | =====2011===== |
+ | ===Roster=== | ||
+ | |Kevin Karplus | karplus@soe.ucsc.edu| Teacher | | ||
+ | |Edward Liaw |eyliaw@soe.ucsc.edu| Student | | ||
+ | |Samuel Vohr |svohr@soe.ucsc.edu| Student | | ||
+ | |Patricia Chan| | Student | | ||
- | jpegtran -rot 90 Jeff.JPG > Jeff.JPG | + | =====2010===== |
- | + | ===Roster=== | |
- | To get a standard screen crop I was using [[http://picasa.google.com/mac/|Picasa]] to do a 4:3 crop (instead of a manual crop) and then saving the image and resizing it. | + | |Kevin Karplus | karplus@soe.ucsc.edu| Teacher, contributor | |
- | + | |Jeff Long | | Student | | |
- | To resize the image to 200x150 you can use **convert**. | + | |Herbert Lee |hlee@soe.ucsc.edu| Student | |
- | + | |Hyunsung John Kim| hyjkim@soe.ucsc.edu| Student | | |
- | convert -size 200x150 Jeff.JPG -resize 200x150 +profile '*' Jeff200.jpg | + | |Michael Cusack| mpcusack@soe.ucsc.edu| Student | |
- | + | |Jonathan Magasin| | Student | | |
- | If you would like me to post your picture and details, feel free to email me a pic and your homepage address, --- //[[jlong@soe.ucsc.edu|Jeff Long]] //. | + | |Dany Steaste | | Student | |
- | + | |Galt Barber | galt@soe.ucsc.edu | Contributor | | |
- | ===== Contributors include the following: ===== | + | |John St. John | jstjohn@soe.ucsc.edu | Student | |
- | + | |Chris Brumbaugh | cbrumbau@soe.ucsc.edu | Student | | |
- | ====Galt Barber==== | + | |Shyamini Vasili | svasili@soe.ucsc.edu | Student | |
- | {{:galt200b.jpg |Galt Barber}} | + | |Jenny Draper | learithe@soe.ucsc.edu | |
- | soe email address: galt | + | |Patricia Chan || |
- | {{editor>?galt&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Michael Cusack==== | + | |
- | mpcusack@soe | + | |
- | {{:michael200b.jpg |Michael Cusack}} | + | |
- | {{editor>?mpcusack&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Jenny Draper==== | + | |
- | {{http://users.soe.ucsc.edu/~learithe/JDraper_Alcatraz_150p.jpg }} | + | |
- | [[http://users.soe.ucsc.edu/~learithe/]] | + | |
- | {{editor>?learithe&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Kevin Karplus==== | + | |
- | {{http://users.soe.ucsc.edu/~karplus/photos/Kevin-head-2008-150x200.jpg |photo of Kevin Karplus}} | + | |
- | [[http://users.soe.ucsc.edu/~karplus]] | + | |
- | {{editor>?karplus&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Jeffrey C. Long==== | + | |
- | {{jeff200b.jpg |Jeffrey C. Long}} | + | |
- | [[http://users.soe.ucsc.edu/~jlong/]] | + | |
- | {{editor>?jlong&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Shyamini Vasili==== | + | |
- | {{shyamini200b.jpg |Shyamini Vasili}} | + | |
- | e-mail id - svasili@soe.ucsc.edu | + | |
- | {{editor>?svasili&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====John St. John==== | + | |
- | {{:johnstjohnhead.gif |Photo of John St. John}} | + | |
- | SOE email: jstjohn\\ | + | |
- | [[http://www.johnstjohn.com/]] | + | |
- | {{editor>?jstjohn&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Chris Brumbaugh==== | + | |
- | {{:chris_brumbaugh_150x200.jpg |Chris Brumbaugh}} | + | |
- | SOE e-mail address: cbrumbau\\ | + | |
- | {{editor>?cbrumbau&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Herbert Lee==== | + | |
- | {{:herbertlee.jpg |Herbert Lee}} | + | |
- | SOE email: hlee\\ | + | |
- | {{editor>?hlee&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + | |
- | + | ||
- | ====Hyunsung John Kim==== | + | |
- | {{:john_kim.jpg |Hyunsung John Kim}} | + | |
- | SOE email: hyjkim\\ | + | |
- | {{editor>?hyjkim&}} | + | |
- | <HTML><br style="clear:both" /><br /><hr /></HTML> | + |