This isn't an exhaustive list of info new people should know, but it will help get you started.
Things to do
- Start a web page: For most people, one goal of working in this lab is to make yourself eligible to stop working in this lab -- that is, to get a job offer (in the case of postdocs and grad students) or to find a good postdoc position (grad and undergrad students). Much of this can be done though doing good science -- publish, publish, publish. But having people who may be interested in you able to find you is also useful -- they should be able to look at your other publications, history, etc. Having your own domain name costs just a few dollars a year and lets your site follow you through your academic path (for example, see this history of brianomeara.info), rather than leave orphaned older versions of your site when you move from place to place. You may also consider more newfangled technology (blogs, social networking, etc.), though remember that anything you publish might become public and visible to people thinking of hiring you (think of how frequently Facebook changes its privacy settings making what was previously private (profile, images, etc.) open by default).
- Set up a backup system. We are setting up a system within the lab, but you should also have an off-site backup system. I personally use CrashPlan (as well as an off-site RAID network storage device, on-site TimeMachine backup to a hard drive, and off-site backups of my main subversion repository [yes, a bit obsessive]), but Mozy, Dropbox, Carbonite, etc. are all viable alternatives. Much of our work is electronic, and it's quite possible to wipe out years of work with a coffee spill unless you have a backup, and an off-site backup is important, too (what if the sprinklers go off in the building? or if there's a fire? or a burglar?).
- Stay organized: I use taskwarrior for keeping track of projects and tasks, but people vary in what works best for them.
- Install necessary software: Assuming you're on a Mac, MacPorts can be handy for installing useful things like Subversion, newer versions of Python or Perl, etc. You'll first need to install Apple's Developer Tools. UTK OIT has site-licensed versions of proprietary programs like MS Office, Endnote, etc. That is also where you can get access to analysis.utk.edu, which has copies of Mathematica, Matlab, and other useful programs
- Investigate local resources: For example, you can have books sent from the library to the EEB satellite office (it's listed as "botany" on the library website). You should learn about the location and resources of NIMBioS (locals pronounce it "nimbus" [like the cloud]). Seminars of interest are typically NIMBios (every other Tuesday) and EEB (every Friday). We also attend lab meetings of the GOG group (Gavrilets, O'Meara, Gilchrist) and the HOFF group (Hulsey, O'Meara, Fordyce, Fitzpatrick). Many members of the department meet at the Sunspot bar on Tuesday and Friday afternoons. The UTK Office of Research has training sessions that are actually quite useful, in contrast to other training experiences you might have had elsewhere. If you have kids, you might check out the Early Learning Center on campus for childcare (apply early); another option some parents have liked is Morning Star Child Development Center, and there are many other options, as well. For new mothers, there are pumping rooms located in the fourth floor women's bathroom in Austin Peay (located just over the enclosed bridge from Hesler) as well as a somewhat nicer one in Ayers Hall across the street.
Key papers
Note that these are key to people in the lab -- it's relevant to know past work in the lab as well as core papers in the field.
- Felsenstein J, 1978. Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading. Systematic Zoology 27:401-410.
- Felsenstein J, 1985. Confidence-Limits on Phylogenies - an Approach Using the Bootstrap. Evolution 39:783-791.
- Felsenstein J, 1985. Phylogenies and the Comparative Method. American Naturalist 125:1-15.
- Felsenstein J, 1988. Phylogenies and Quantitative Characters. Annual Review of Ecology and Systematics 19:445-471.
- Pagel M, 1994. Detecting Correlated Evolution on Phylogenies - a General-Method for the Comparative-Analysis of Discrete Characters. Proceedings of the Royal Society of London Series B-Biological Sciences 255:37-45.
- Hansen TF, Martins EP, 1996. Translating between microevolutionary process and macroevolutionary patterns: The correlation structure of interspecific data. Evolution 50:1404-1417.
- Maddison WP, 1997. Gene trees in species trees. Systematic Biology 46:523-536.
- Pagel M, 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26:331-348.
- Schluter D, Price T, Mooers AO, Ludwig D, 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
- Cunningham CW, Omland KE, Oakley TH, 1998. Reconstructing ancestral character states: a critical reappraisal. Trends in Ecology & Evolution 13:361-366.
- Maddison WP, Knowles LL, 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55:21-30.
- O'Meara BC, Ane C, Sanderson MJ, Wainwright PC, 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
- Maddison WP, Midford PE, Otto SP, 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56:701-710.
- O'Meara BC, 2010. New Heuristic Methods for Joint Species Delimitation and Species Tree Inference. Systematic Biology 59:59-73.
Key books
- Origin of Species by Darwin [No, don't just have it on your shelf: read it!]
- Inferring Phylogenies by Felsenstein
- Phylogenetics by Semple and Steel may be useful to certain lab members
- Computational Molecular Evolution by Yang
Key languages
Key applications
Key unix commands
- ssh
- scp
- rm
- mkdir
- grep
- vi (see cheat sheet)
- less
- top
- head
- tail
- hg
- svn
- rsync
This isn't an exhaustive list of info new people should know, but it will help get you started.
Things to do
- Start a web page: For most people, one goal of working in this lab is to make yourself eligible to stop working in this lab -- that is, to get a job offer (in the case of postdocs and grad students) or to find a good postdoc position (grad and undergrad students). Much of this can be done though doing good science -- publish, publish, publish. But having people who may be interested in you able to find you is also useful -- they should be able to look at your other publications, history, etc. Having your own domain name costs just a few dollars a year and lets your site follow you through your academic path (for example, see this history of brianomeara.info), rather than leave orphaned older versions of your site when you move from place to place. You may also consider more newfangled technology (blogs, social networking, etc.), though remember that anything you publish might become public and visible to people thinking of hiring you (think of how frequently Facebook changes its privacy settings making what was previously private (profile, images, etc.) open by default).
- Set up a backup system. We are setting up a system within the lab, but you should also have an off-site backup system. I personally use CrashPlan (as well as an off-site RAID network storage device, on-site TimeMachine backup to a hard drive, and off-site backups of my main subversion repository [yes, a bit obsessive]), but Mozy, Dropbox, Carbonite, etc. are all viable alternatives. Much of our work is electronic, and it's quite possible to wipe out years of work with a coffee spill unless you have a backup, and an off-site backup is important, too (what if the sprinklers go off in the building? or if there's a fire? or a burglar?).
- Stay organized: I use taskwarrior for keeping track of projects and tasks, but people vary in what works best for them.
- Install necessary software: Assuming you're on a Mac, MacPorts can be handy for installing useful things like Subversion, newer versions of Python or Perl, etc. You'll first need to install Apple's Developer Tools. UTK OIT has site-licensed versions of proprietary programs like MS Office, Endnote, etc. That is also where you can get access to analysis.utk.edu, which has copies of Mathematica, Matlab, and other useful programs
- Investigate local resources: For example, you can have books sent from the library to the EEB satellite office (it's listed as "botany" on the library website). You should learn about the location and resources of NIMBioS (locals pronounce it "nimbus" [like the cloud]). Seminars of interest are typically NIMBios (every other Tuesday) and EEB (every Friday). We also attend lab meetings of the GOG group (Gavrilets, O'Meara, Gilchrist) and the HOFF group (Hulsey, O'Meara, Fordyce, Fitzpatrick). Many members of the department meet at the Sunspot bar on Tuesday and Friday afternoons. The UTK Office of Research has training sessions that are actually quite useful, in contrast to other training experiences you might have had elsewhere. If you have kids, you might check out the Early Learning Center on campus for childcare (apply early); another option some parents have liked is Morning Star Child Development Center, and there are many other options, as well. For new mothers, there are pumping rooms located in the fourth floor women's bathroom in Austin Peay (located just over the enclosed bridge from Hesler) as well as a somewhat nicer one in Ayers Hall across the street.
Key papers
Note that these are key to people in the lab -- it's relevant to know past work in the lab as well as core papers in the field.
- Felsenstein J, 1978. Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading. Systematic Zoology 27:401-410.
- Felsenstein J, 1985. Confidence-Limits on Phylogenies - an Approach Using the Bootstrap. Evolution 39:783-791.
- Felsenstein J, 1985. Phylogenies and the Comparative Method. American Naturalist 125:1-15.
- Felsenstein J, 1988. Phylogenies and Quantitative Characters. Annual Review of Ecology and Systematics 19:445-471.
- Pagel M, 1994. Detecting Correlated Evolution on Phylogenies - a General-Method for the Comparative-Analysis of Discrete Characters. Proceedings of the Royal Society of London Series B-Biological Sciences 255:37-45.
- Hansen TF, Martins EP, 1996. Translating between microevolutionary process and macroevolutionary patterns: The correlation structure of interspecific data. Evolution 50:1404-1417.
- Maddison WP, 1997. Gene trees in species trees. Systematic Biology 46:523-536.
- Pagel M, 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26:331-348.
- Schluter D, Price T, Mooers AO, Ludwig D, 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
- Cunningham CW, Omland KE, Oakley TH, 1998. Reconstructing ancestral character states: a critical reappraisal. Trends in Ecology & Evolution 13:361-366.
- Maddison WP, Knowles LL, 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55:21-30.
- O'Meara BC, Ane C, Sanderson MJ, Wainwright PC, 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
- Maddison WP, Midford PE, Otto SP, 2007. Estimating a binary character's effect on speciation and extinction. Systematic Biology 56:701-710.
- O'Meara BC, 2010. New Heuristic Methods for Joint Species Delimitation and Species Tree Inference. Systematic Biology 59:59-73.
Key books
- Origin of Species by Darwin [No, don't just have it on your shelf: read it!]
- Inferring Phylogenies by Felsenstein
- Phylogenetics by Semple and Steel may be useful to certain lab members
- Computational Molecular Evolution by Yang
Key languages
Key applications
Key unix commands
- ssh
- scp
- rm
- mkdir
- grep
- vi (see cheat sheet)
- less
- top
- head
- tail
- hg
- svn
- rsync