The Goldschmidt 2012 meeting abstract deadline is rapidly approaching (Feb 1), and I'm organizing a geomicrobiology session with Jennifer Bowen (U Mass Boston). The conferences will be held in Montreal (!!) this year, from June 24-29.
Any questions? Don't hesitate to contact me!
Goldschmidt 2012 session 16b: "Omics and geomicrobiology: examining microbe-mineral interactions using cutting-edge microbiological methods"
Geomicrobiologists contend with unusual challenges in assessing microbial communities and their activity in sediment, soil and on rock substrates. These often include complex matrices, high metal concentrations, and low biomass. Microbial communities are frequently stratified over minute spatial scales; molecular microbiological methods such as next-gen sequencing techniques and single cell genomics are powerful tools we can use to tease out geomicrobiological relationships in these environments. In this session, we aim to bring together researchers that use “omics” and other cutting edge microbiological methods in their studies of microbial communities and microbially-mediated elemental and mineral transformations. Submissions using multidisciplinary approaches incorporating one or more of these methods in field or applied studies are particularly welcome, for example studies of radionuclide and toxic metal remediation, environmental analogues of early earth, carbon sequestration, bioleaching, and elemental transformations in soils, sediments, or on mineral surfaces.
Our featured presenters are:
Peter Girguis(Harvard) “Hot-wired: the role of extracellular electron transfer in sustaining primary production by hydrothermal vent microbes”
Karen Lloyd (University of Tennesse-Knoxville)
Jenn Macalady(Pennsylvania State University)
The abstract deadline is 1 Feb 2012. Further information on abstract content and formatting, and an on-line submissions link can be found on the Goldschmidt website at http://www.vmgoldschmidt.org/2012/abstracts.htm.
Hope to see you there!
Tuesday, January 24, 2012
Tuesday, September 27, 2011
um no more! Getting smart with autocorrect, for scientists
Had enough of searching for μ, °, β, ζ, etc in the symbols or special characters dialogue boxes of word or open office write? There is an easier way!
This already exists elsewhere on the internet, I'm basically paraphrasing from a combo of the office website and an open office blog. I thought it might be useful for other scientists to see these pages distilled down to a science specific version so here you go!
MS word (this should work equally well in old word and Word 2007)
1. go to the insert tab, click symbol. The symbol dialogue box/window should appear. click on the symbols or special characters tab in Word 2007.
2. find the μ (mu) symbol (under greek alphabet) or whatever symbol you are pining for. click on it, then click the autocorrect button. The autocorrect window will appear.
3. Your μ should appear under "with". Click plain text next to "with" and edit the with box to your desired result (e.g. μM).
4. To the left of the "with" box is the "replace" box, type whatever you want to replace with μM in this box. e.g. um.
5. click add, and ok to exit the window. Test it!
Note there is a potential for confusion in the um department (μm vs μM). You can only set one up to autocorrect, however once it is autocorrected you can manually replace the m with M or vice versa if need be. Or you can set up to replace \mu and with the symbol alone. Up to you!
Open Office write: (NOTE: this *should* work, but it didn't work for me. I'll see if I can find more on this, might be that my version of writer has a bug)
1. Under the insert tab, click special characters. In the dialogue box that appears, select and insert the special character of your choice into the document, press ok to exit the box. Note μ is under the subset basic greek, and ° and serveral other useful symbols are under subset Latin-1.
2. Select the symbol.
3. Go to the tools tab, then click autocorrect options. In the dialogue box that opens up, your symbol will be in the "with" box. If it isn't, go back to step 2 and try again.
4. Type the string of text you want to replace in the "replace" box, and edit the with box if necessary. Click new to add the new autocorrection, and then ok.
5. test it.
This already exists elsewhere on the internet, I'm basically paraphrasing from a combo of the office website and an open office blog. I thought it might be useful for other scientists to see these pages distilled down to a science specific version so here you go!
MS word (this should work equally well in old word and Word 2007)
1. go to the insert tab, click symbol. The symbol dialogue box/window should appear. click on the symbols or special characters tab in Word 2007.
2. find the μ (mu) symbol (under greek alphabet) or whatever symbol you are pining for. click on it, then click the autocorrect button. The autocorrect window will appear.
3. Your μ should appear under "with". Click plain text next to "with" and edit the with box to your desired result (e.g. μM).
4. To the left of the "with" box is the "replace" box, type whatever you want to replace with μM in this box. e.g. um.
5. click add, and ok to exit the window. Test it!
Note there is a potential for confusion in the um department (μm vs μM). You can only set one up to autocorrect, however once it is autocorrected you can manually replace the m with M or vice versa if need be. Or you can set up to replace \mu and with the symbol alone. Up to you!
Open Office write: (NOTE: this *should* work, but it didn't work for me. I'll see if I can find more on this, might be that my version of writer has a bug)
1. Under the insert tab, click special characters. In the dialogue box that appears, select and insert the special character of your choice into the document, press ok to exit the box. Note μ is under the subset basic greek, and ° and serveral other useful symbols are under subset Latin-1.
2. Select the symbol.
3. Go to the tools tab, then click autocorrect options. In the dialogue box that opens up, your symbol will be in the "with" box. If it isn't, go back to step 2 and try again.
4. Type the string of text you want to replace in the "replace" box, and edit the with box if necessary. Click new to add the new autocorrection, and then ok.
5. test it.
Monday, August 1, 2011
AGU session on microbe-mineral interactions!
The AGU fall meeting abstract deadline is rapidly approaching(Aug 4) - check out our session! I'm organizing this session with Clara Chan (U Delaware) and Kim Handley (UC-Berkeley). Any questions? Don't hesitate to contact me!
AGU 2011 session B51: Microbe-Mineral Interactions in Modern and Ancient Environments
To understand biogeochemical processes, we must link microbial metabolism to elemental transformations. We still have much to learn about the identity of key microbes, biosignatures, effects of microbial community interactions, and biochemical mechanisms driving element cycling. In this session, we aim to bring together researchers that study biomineral formation and dissolution in modern environments, with applications to topics such as bioremediation and modeling of ancient biogeochemistry. We welcome submissions on cutting-edge, multidisciplinary approaches to study metal and sulfur biogeochemistry, controls on elemental transformations, and the ecology and evolution of relevant organisms and functional genes.
Our featured presenters are:
John Bargar (SSRL)
David Emerson (Bigelow Lab for Ocean Sciences)
Robin Gerlach (Montana State)
Alexis Templeton (CU-Boulder)
The abstract deadline is 4 August 2011. Further information on abstract content and formatting, and an on-line submissions link can be found on the AGU website at http://sites.agu.org/fallmeeting/scientific-program/submit-policies/.
More information about the conference is also available online at http://sites.agu.org/fallmeeting/.
AGU 2011 session B51: Microbe-Mineral Interactions in Modern and Ancient Environments
To understand biogeochemical processes, we must link microbial metabolism to elemental transformations. We still have much to learn about the identity of key microbes, biosignatures, effects of microbial community interactions, and biochemical mechanisms driving element cycling. In this session, we aim to bring together researchers that study biomineral formation and dissolution in modern environments, with applications to topics such as bioremediation and modeling of ancient biogeochemistry. We welcome submissions on cutting-edge, multidisciplinary approaches to study metal and sulfur biogeochemistry, controls on elemental transformations, and the ecology and evolution of relevant organisms and functional genes.
Our featured presenters are:
John Bargar (SSRL)
David Emerson (Bigelow Lab for Ocean Sciences)
Robin Gerlach (Montana State)
Alexis Templeton (CU-Boulder)
The abstract deadline is 4 August 2011. Further information on abstract content and formatting, and an on-line submissions link can be found on the AGU website at http://sites.agu.org/fallmeeting/scientific-program/submit-policies/.
More information about the conference is also available online at http://sites.agu.org/fallmeeting/.
Tuesday, February 8, 2011
Journal Coffee - a new take on an old challenge
Organizing a regular journal club is a real challenge - despite there being a generally positive attitude about it around these parts, momentum often flags in a major way. At our lab it is difficult to get a crowd together. People are often traveling, on research cruises, at meetings, overwhelmingly busy with their own work in the lab or up against the deadlines writing proposals and papers - meeting up every two weeks as a group is very difficult to coordinate!
This year, in an effort to try to inject some fresh dynamic energy into journal club, I’m introducing something new - journal coffee (or beverage of your choice).
The idea with journal coffee is to:
a. get people together for coffee, something we don’t do too often anyway (everyone is too busy working hard!)
b. expose ourselves to current literature, in a casual and low pressure setting.
c. Not spend too much time on it - attendees should not have to worry that they’ll get lured into a long, drawn-out discussion they can’t escape. 20-30 min max.
c. identify papers where the group interest is high enough to warrant a more in depth journal club meeting.
I’m not sure it people would turn out to this but I think it is worth a try - in the worst case scenario, I drink a cup of coffee by myself, which I’m going to do anyway so what have I got to lose.
This year, in an effort to try to inject some fresh dynamic energy into journal club, I’m introducing something new - journal coffee (or beverage of your choice).
The idea with journal coffee is to:
a. get people together for coffee, something we don’t do too often anyway (everyone is too busy working hard!)
b. expose ourselves to current literature, in a casual and low pressure setting.
c. Not spend too much time on it - attendees should not have to worry that they’ll get lured into a long, drawn-out discussion they can’t escape. 20-30 min max.
c. identify papers where the group interest is high enough to warrant a more in depth journal club meeting.
I’m not sure it people would turn out to this but I think it is worth a try - in the worst case scenario, I drink a cup of coffee by myself, which I’m going to do anyway so what have I got to lose.
Wednesday, January 26, 2011
2011 - geomicro relevant conferences and workshops on the horizon
Pondering my options... and wishing I could go to the rest! This is a work in progress, feel free to suggest additions.
Conferences:
Gordon Conference: Geobiology. January 30 - February 4, 2011.
http://www.grc.org/programs.aspx?year=2011&program=geobiology
Goldschmidt 2011, Prague, Czech Republic, 14-19 Aug 2011, Abstracts due before 15 April
http://goldschmidt2011.org/
ISEB 20: Frontiers in Biogeochemistry, Istanbul, Turkey, 27-30 Sept 2011. Abstracts due before 30 April.
http://www.isebiogeochemistry.com/ISEB_20.htm
Keystone Symposium: Microbial Communities as Drivers of Ecosystem Complexity, 25 - 30 March 2011, Breckenridge, Colorado. Registration deadline: 25 March 2011.
http://www.keystonesymposia.org/meetings/viewMeetings.cfm?MeetingID=1059
other Keystone symposia: http://www.keystonesymposia.org/default.cfm
ASLO meetings: http://aslo.org/meetings/aslomeetings.html
NACE: Corrosion conferences etc http://www.nace.org/content.cfm?parentid=1006¤tID=1006
Workshops/Shortcourses:
MSU Microbial Metagenomics Course, East Lansing, Michigan. 12-25 June 2011.
http://www.mmg.msu.edu/
Conferences:
Gordon Conference: Geobiology. January 30 - February 4, 2011.
http://www.grc.org/programs.aspx?year=2011&program=geobiology
Goldschmidt 2011, Prague, Czech Republic, 14-19 Aug 2011, Abstracts due before 15 April
http://goldschmidt2011.org/
ISEB 20: Frontiers in Biogeochemistry, Istanbul, Turkey, 27-30 Sept 2011. Abstracts due before 30 April.
http://www.isebiogeochemistry.com/ISEB_20.htm
Keystone Symposium: Microbial Communities as Drivers of Ecosystem Complexity, 25 - 30 March 2011, Breckenridge, Colorado. Registration deadline: 25 March 2011.
http://www.keystonesymposia.org/meetings/viewMeetings.cfm?MeetingID=1059
other Keystone symposia: http://www.keystonesymposia.org/default.cfm
ASLO meetings: http://aslo.org/meetings/aslomeetings.html
NACE: Corrosion conferences etc http://www.nace.org/content.cfm?parentid=1006¤tID=1006
Workshops/Shortcourses:
MSU Microbial Metagenomics Course, East Lansing, Michigan. 12-25 June 2011.
http://www.mmg.msu.edu/
Short Course: Tools in Environmental Biogeochemistry - Opportunities and Limitations, University of Tuebingen, Germany. Application due: 31 Jan 2011.
4 day workshop organized by Thomas Borch (Colorado), Ruben Kretzschmar (RTH Zürich) and Andreas Kappler. It will present and discuss the application of several spectroscopic and microscopic techniques in environmental biogeochemistry.
Thursday, December 16, 2010
tapping the trees of knowledge that are webinars
Webinars are such an amazing educational opportunity, and a great way to gather useful tips and insight on new (or new to you) lab techniques. Here are some links to a few I've watched, and some I hope to watch sometime soon. What a great resource, I am so enamoured with webinars!
If you have others to suggest, please let me know, this is a work in progress.
AAAS/Science: AAAS has put up a variety of webinars, definitely leaning toward biomedical interests from what I can see, but there are still a few useful ones for the geomicrobiologically inclined. I watched the webinar on the qPCR MIQE guidelines a few months ago. It was really well put together, the presentations were by experts in the field, with practical suggestions, and a chance for feedback from those watching the presentations. Plus you can view them anytime after the presentation on the AAAS/Science website: http://www.sciencemag.org/site/marketing/webinar/
Sigma-Aldrich: Sigma and co have put up a barrage of webinars. I've watched a few on qPCR and I thought they were great, they range from beginner to expert level. They also offer webinars on topics such as HPLC, proteomics, and synthetic chemistry. Hopefully more webinars are coming? Hint hint Sigma! I found their sign up and log in procedure for the qPCR seminars was a bit maddening but worth the time (I think if you bookmark each seminar you can skip the hassle of signing in too!)
NACE webinars: corrosion themed, one to explore http://events.nace.org/webinars/OnDemand/upcoming.asp
APECS webinars - weekly career development webinars from the Association of Polar Early Career Scientists. Easy sign up, user friendly interface with chat, the speaker will address viewers chat comments in real time. Small enough groups that during the Q&A session your questions will get answered! Past webinars are archived and can be watched on demand. More info here: http://apecs.is/webinars
to be continued....
If you have others to suggest, please let me know, this is a work in progress.
AAAS/Science: AAAS has put up a variety of webinars, definitely leaning toward biomedical interests from what I can see, but there are still a few useful ones for the geomicrobiologically inclined. I watched the webinar on the qPCR MIQE guidelines a few months ago. It was really well put together, the presentations were by experts in the field, with practical suggestions, and a chance for feedback from those watching the presentations. Plus you can view them anytime after the presentation on the AAAS/Science website: http://www.sciencemag.org/site/marketing/webinar/
Sigma-Aldrich: Sigma and co have put up a barrage of webinars. I've watched a few on qPCR and I thought they were great, they range from beginner to expert level. They also offer webinars on topics such as HPLC, proteomics, and synthetic chemistry. Hopefully more webinars are coming? Hint hint Sigma! I found their sign up and log in procedure for the qPCR seminars was a bit maddening but worth the time (I think if you bookmark each seminar you can skip the hassle of signing in too!)
NACE webinars: corrosion themed, one to explore http://events.nace.org/webinars/OnDemand/upcoming.asp
APECS webinars - weekly career development webinars from the Association of Polar Early Career Scientists. Easy sign up, user friendly interface with chat, the speaker will address viewers chat comments in real time. Small enough groups that during the Q&A session your questions will get answered! Past webinars are archived and can be watched on demand. More info here: http://apecs.is/webinars
to be continued....
Saturday, February 20, 2010
Writing for the peer reviewed literature - get that first draft moving!
A few weeks ago I discovered a new weapon to add to my writing arsenal. Whatever your scientific discipline, I think you (or your students) might find this exercise helpful for writing papers for peer reviewed publication. The tool is the Applied and Environmental Microbiology (AEM) short form article: http://aem.asm.org/misc/journal-ita_org.dtl#04
Whether or not you plan to actually submit a paper to AEM in this format, writing a short form paper draft can be a useful method to tackle a manuscript, especially if you have trouble getting started.
The basic format is:
Title (keep it short)
Running Title (54 characters and spaces max)
Abstract (50 words max)
Body (1000 words max, no section breaks, combine methods, results and discussion)
Figures and tables (kept to a minimum)
References
The beauty of the short form AEM paper is it is SHORT. so you have to distill your thoughts down to the essential. The strict word limit really force you to focus your presentation. For example: 50 word abstract (!!). Initially, I misread the title requirements and though the running title limit was the character limit on the title - this is actually a great exercise too, it is very hard to compose a 54 character title! Maybe a bit too hard - but it does force you to be as succinct and relevant as possible.
Within a few hours you can have a rough draft in your hands. If you are unsure about the direction you want the paper to take, you can write another one. Why not try out different ways to present your work and determine the most appropriate and relevant way to present your results? The AEM short draft format is probably not the format you'll stick with for your second draft or onwards. Chances are your final product will need to be much longer and divided into sections (intro, methods, results, discussion). Thus, it is much easier to explore the presentation approach for your work at the first draft stage where the manuscript is short and easy to follow, then in later drafts where you can get lost in the forest of information presented.
If nothing else, using this method can help you get that first draft on the table to work from - better to start from somewhere than nowhere!
Whether or not you plan to actually submit a paper to AEM in this format, writing a short form paper draft can be a useful method to tackle a manuscript, especially if you have trouble getting started.
The basic format is:
Title (keep it short)
Running Title (54 characters and spaces max)
Abstract (50 words max)
Body (1000 words max, no section breaks, combine methods, results and discussion)
Figures and tables (kept to a minimum)
References
The beauty of the short form AEM paper is it is SHORT. so you have to distill your thoughts down to the essential. The strict word limit really force you to focus your presentation. For example: 50 word abstract (!!). Initially, I misread the title requirements and though the running title limit was the character limit on the title - this is actually a great exercise too, it is very hard to compose a 54 character title! Maybe a bit too hard - but it does force you to be as succinct and relevant as possible.
Within a few hours you can have a rough draft in your hands. If you are unsure about the direction you want the paper to take, you can write another one. Why not try out different ways to present your work and determine the most appropriate and relevant way to present your results? The AEM short draft format is probably not the format you'll stick with for your second draft or onwards. Chances are your final product will need to be much longer and divided into sections (intro, methods, results, discussion). Thus, it is much easier to explore the presentation approach for your work at the first draft stage where the manuscript is short and easy to follow, then in later drafts where you can get lost in the forest of information presented.
If nothing else, using this method can help you get that first draft on the table to work from - better to start from somewhere than nowhere!
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