wikis were first envisioned as collaborative information repositories ( cir ) for the distributed annotation and re - annotation of genomes in model organism databases ( mods ) more than 10 years ago ( 1 ) .
an online wiki - style cir mod offers the potential to solve three challenges confronted by many smaller model organism communities in the post - genomic era ( 2 ) .
the first is the ongoing dependence of biological databases , including mods , on constant federal support for proper maintenance and curation ( 3 ) . as databases proliferated over the past decade , many reached critical cross - roads : funding organizations that supported their design and implementation were anxious to wean them off the federal funding stream for maintenance and updates .
the second challenge is to develop an effective means to engage more undergraduate students in real genomics research .
undergraduates represent a large and enthusiastic group that can make meaningful advances in many areas of science ( 4 ) , and genome annotation provides an excellent opportunity to realize this potential ( 5 ) .
this approach was first used to annotate the genome of the plant pathogen agrobacterium tumefaciens c58 ( 6 ) . since then , there have been several additional annotation projects involving undergraduate students ( 5,79 ) . given these successes , it is somewhat surprising that the process has not been more widely adopted .
the projects serve as a mechanism for undergraduate students to interact with researchers , contribute to genome annotations and see the impact of those contributions .
the third challenge faced by model organism communities is that , more often than not , researchers who study the model organism perceive that they have little or no direct participation in the annotation of its genome .
errors in the genbank file for an organism s genome persist , sometimes for years , even though any member of that organism s research community could correct it with a few simple edits .
wikis were seen as a means of directly engaging a research community in the continual process of re - annotation , thereby offering a path to more accurate and up - to - date genomes ( 10 ) . our original goal with xanthusbase was to address each of these three problems .
in 2005 , at the 32nd international conference on the biology of the myxobacteria , the research community that studies myxococcus xanthus expressed unanimous support for the creation of an accessible , inexpensive wiki - style cir mod , and several principle investigators ( pis ) also expressed interest in the educational potential of such a mod . from its first iteration
, the xanthusbase user interface was designed to be familiar to anyone who has used a mod .
the genome annotation was parsed into genepages , each of which represented one open reading frame ( orf ) .
genepages were arranged in order along the genome , which was represented as a single circular chromosome .
any registered user could update the annotation by editing a genepage , with the following three caveats : all edits would be identified by author ; all edits would be saved forever ; and any user could return to a previous edit with a single mouse click .
there are larger and more comprehensive databases that include information about the m. xanthus genome , such as ncbi ( 11 ) , jcvi ( http://www.jcvi.org/ ) , biocyc ( 12 ) and many others .
xanthusbase aggregates information from some of them , such as pfam ( 13 ) , kegg ( 14 ) and go ( 15 ) , and reproduces some of the features of others , but its function as an autonomous community - owned and operated wiki - style cir mod remains unique .
the continuous support of the community of researchers who study m. xanthus as a model organism , as well as interest from other small model organism communities , indicates that this system can play a unique role in supporting research and education .
since the original publication , we have made major improvements , many of which are not immediately obvious .
the previous version required manual installation onto a server , but this made it difficult to create exact replica test servers for update development .
the resulting installer and website software were general enough that it can be used to create a mod for any bacterium that : ( i ) has a single circular chromosome , ( ii ) has an existing genbank file and ( iii ) is listed in kegg . since the software is no longer specific to m. xanthus we renamed it openmods ; xanthusbase now refers to the installation of openmods for m. xanthus .
an openmods installation requires a dedicated computer or virtual machine that runs debian or ubuntu and a dedicated network connection .
the first installs the software dependencies that openmods requires using the automated software installer present in debian and ubuntu ( apt ) .
the second command asks the user for some information ( using debconf ) about the specific installation .
after about 10 min the website has acquired most of the information from external sources and is ready to be viewed .
it takes about a week for the website to complete its first update of all information from external sources .
figure 1 gives a high level view of how information enters and exits the database . 

the genbank file is automatically downloaded via ftp , and the following information is then parsed from it : locus , coordinates , length , strand , gene name , gene products , note and sequence .
users are allowed to edit most of the fields , but gene name , gene products and note are the only ones saved to the updated genbank file .
the genbank file is automatically downloaded via ftp , and the following information is then parsed from it : locus , coordinates , length , strand , gene name , gene products , note and sequence .
users are allowed to edit most of the fields , but gene name , gene products and note are the only ones saved to the updated genbank file .
the first is to set up the header ; the user must provide a website name , pi information and institution logo .
the top of figure 2 shows the header of the openmods installation specific to xanthusbase . on the left hand side
xanthusbase with the subtitle :  myxococcus xanthus dk1622 and related bacteria. this is a graphic that is automatically created by a java program in the installer . on the right hand side
after installation , this information can be updated using a command ( $ openmods configure ) . 

figure 2.openmods genepage screenshot . from top to bottom , the genepage contains : geneome browser , locus ( static ) , coordinates ( static ) , gene length ( static ) , strand ( static ) , gene name ( editable ) , gene products ( editable ) , note ( editable ) , motifs ( periodically updated but not editable ) , pathways ( periodically updated but not editable ) , go information ( periodically updated but not editable ) , mutant strains ( editable ) , protein synonyms ( editable ) , gene synonyms ( editable ) , mutant phenotypes ( editable ) and community description ( editable ) .
the genepage also contains the protein and nucleotide sequence but is not shown due to space constraints .
openmods genepage screenshot . from top to bottom , the genepage contains : geneome browser , locus ( static ) , coordinates ( static ) , gene length ( static ) , strand ( static ) , gene name ( editable ) , gene products ( editable ) , note ( editable ) , motifs ( periodically updated but not editable ) , pathways ( periodically updated but not editable ) , go information ( periodically updated but not editable ) , mutant strains ( editable ) , protein synonyms ( editable ) , gene synonyms ( editable ) , mutant phenotypes ( editable ) and community description ( editable ) .
the genepage also contains the protein and nucleotide sequence but is not shown due to space constraints .
the user is required to enter three pieces of information : the ftp location of the genbank file , the kegg organism abbreviation and a name for the organism to be displayed in the  select organism dropdown menu .
after the first organism is specified the installer continues onto the data backup section , but additional organisms can be installed on an openmods installation using the command ( $ openmods new_organism ) .
organisms can also be deleted using ( $ openmods delete_organism ) the third step is for the user to specify how data backup will be performed .
if this option is selected , the user should insert a blank , 4  gb ( minimum ) flash drive into any usb port on the computer . once a week the automatic backup daemon will run and detect any flash drives plugged into the system and push backups there . even if the entire computer hosting an openmods installation
is destroyed beyond repair , everything needed to recreate an installation is present on the flash drive , including usernames and user annotations .
the procedure to install on a new computer from backup is : install a fresh copy of openmods , do not specify an organism and run the command ( $ openmods import
a backup can be triggered outside of the routine by running a command ( $ openmods backup ) .
this is useful if openmods is installed on a virtual machine where the administrator has no physical access , and therefore can not plug in a flash drive . the administrator can change these settings at any time using the command ( $ openmods backup_setup ) .
information is still organized according to genepages , where each genepage represents one orf , and genepages are organized by their location in the genome .
figure 2 shows a representative genepage , where information can be grouped into sections from top to bottom .
the first section is the genome browser , which is a clickable image showing nearby orfs .
a user can click an orf in the genome browser and go to its genepage , or can scroll left or right along the chromosome by clicking on the left or right arrows the genome browser was developed from scratch because existing genome browsers , specifically , gbrowse ( http://gmod.org/wiki/gbrowse ) require user intervention to install and do not integrate with the openmods installer .
this section contains orf locus , coordinates , length , strand , gene name , gene products and note ; gene name , gene products and note are the only editable fields in this section .
the third section contains motif , pathway and gene ontology data ; none of this information is editable by the user .
motif and pathway information is updated automatically from kegg once a month , and the gene ontology information is updated using blast2go , also once a month .
the fourth section contains fields that allow researchers to register mutant strains ( suggested by the m. xanthus community at the 38th annual international conference on the biology of myxobacteria ) .
the fifth section contains information that is not in the genbank file , but may be useful to the community , such as protein synonyms , gene synonyms , mutant phenotypes and community description .
although none of the fields in this section are written out to an updated genbank file , they are saved during backup .
it is not necessary to register in order to see xanthusbase and browse the annotation ; however , those who wish to add information must register .
access and security are managed by designating four types of users with different permission levels : blocked user , student , researcher and principle investigator .
a person who registers with xanthusbase will be a blocked user until their permission level is changed ( to prevent web bots from destroying the integrity of the database ) .
student may contribute changes to the annotation , but these changes are marked as pending until approved by a user with permission level 
researcher my make changes to the annotation without approval , and may approve or deny any suggested student - level changes .
users with permission level  principle investigator may do everything a researcher can do , and in addition can delete users , change their permission level , create groups of users according to laboratories or classes , and download a group s media ( pdf s , images and videos ) as a zip file with one folder per user in the group .
 principle investigator and  researcher contributions , as well as student proposed contributions , are visible for each orf on its respective genepage , and they are also compiled on a list of recent changes . although the entire history of changes is stored in the database in perpetuity , a user has the ability to immediately undo a change in the event of an input error .
a genbank file for the organism that incorporates all of the most recent changes can be downloaded using the command ( $ openmods genbank_out ) .
the discussion examines openmods as a solution to each of the three problems stated in the introduction , using xanthusbase as an example .
it depends on only free software , is itself entirely free and open source , and can be installed on inexpensive hardware .
joomla is used to allow administrators to change user s passwords and the static text on the site . for hardware ,
we recommend a computer with at least one 32-bit cpu core and 2  gb of ram .
we have tested the current version of openmods to ensure its reliability . over the past year
, xanthusbase has been running 24    7 on the hardware configuration specified and received between 20 and 100 unique visitors per day .
it can handle loads of at least 30 users simultaneously ( all of the students in our class have simultaneously logged in and used the website ) .
significant efforts have been made to ensure that the database remains secure . in all cases
where content is uploaded according to a user level , openmods conducts server - side checks for permissions .
the site protects against sql - injection attacks for all data that can touch an sql query .
it also protects against command line escaping when calling java - based programs for backend processing .
user passwords are stored as md5 hashes with salt by joomla so that even people with administrator access can not view a user s password .
for the past 5 years , we have taught an introductory bioinformatics class designed for upper - division undergraduate students with a strong background in molecular biology but limited computer skills .
its purpose is to present a subset of the fundamental file formats , algorithms and databases in sufficient detail that the students are able not only to identify and apply them , but also to make informed and critical interpretations .
our curriculum has lecture and computer laboratory components that teach genome annotation , and students must then apply this knowledge in interactive research .
each lecture provides background for the subsequent laboratory , which ultimately leads to a final project where students contribute to the re - annotation of a bacterial genome ( usually , but not always m. xanthus ) .
we introduced a re - annotation exercise into the course using xanthusbase in 2009 . in 2011
we greatly expanded the role of xanthusbase , due both to curriculum development and the aforementioned significant software redesign .
for the final project , students were assigned approximately 50 orfs from the m. xanthus genome and asked to perform a thorough and documented re - annotation using xanthusbase .
the quality of the 2011 student annotations exceeded our expectations , thus improving the annotation for 136 orf s when compared to the current m. xanthus genbank file ( http://www.ncbi.nlm.nih.gov/nuccore/108460647 ) .
approximately 65% of the contributions were approved as being meaningful , with the most productive student improving the annotation of all 50 reading frames she was assigned .
all contributions remain on xanthusbase and can be viewed by anyone ( select organism / myxococcus xanthus / recent annotations ) .
the expected area of impact where we have encountered the most challenges has been in engaging the m. xanthus research community in active , collaborative genome annotation through xanthusbase .
while certainly some researchers and students have made meaningful contributions , there have been far fewer than was originally envisioned .
we believe that this does not reflect negatively on openmods , which has proven itself over the past 5 years to be a reliable mod and an extremely useful teaching tool , and we certainly do not believe it reflects negatively on the community of m. xanthus researchers , who represent a truly dedicated and collaborative group .
wiki - style databases have proven to be a highly effective means of collecting and organizing information under certain circumstances , but they are not always the best option .
the barriers to collaborative genome annotation have been discussed , and these remain unchanged since life science wikis began to proliferate . although there has been no rigorous examination as to why academic researchers do not embrace wiki - style cirs , there are reasons that seem obvious to an inside observer .
academic research takes place within an established incentive structure defined by a series of goals : a tenure - track job , research funding , tenure and promotion .
contributions to a wiki - style cir do not move a researcher closer to these goals .
in fact , such contributions may actually function as a hindrance , since data contributed to a wiki - style cir might be considered published and therefore ineligible for subsequent publication in a peer - reviewed journal .
even if that were not the case , explaining your ideas pre - publication in an online forum could be viewed as potentially helping your competitors .
michel aaij at auburn university montgomery recently used his more than 60  000 contributions to wikipedia as part of his tenure portfolio ( http://blog.wikimedia.org/2011/04/06/tenure-awarded-based-in-part-on-wikipedia-contributions ) , but at present he represents an extreme outlier . although pis may not have an adequate incentive to contribute to a wiki - style cir mod , perhaps graduate students and post - doctoral fellows would contribute ?
since they are already experts , it could be argued that contributing would require little additional effort .
unfortunately , in a study that analyzed the effect of wikis on student writing , wheeler et al .
( 16 ) found that students who contributed to wikis were cognizant that their contributions lacked anonymity , and would be read by peers , and that this caused them to spend more time and write more carefully than usual for their assignments .
the same is likely to apply to graduate students and post - doctoral fellows contributing to a wiki - style cir mod that might be read by their peers , pi and other members of the scientific community . perhaps because of this , they would feel the need to devote considerable time and effort to their contributions , and thus may arrive at the conclusion that this time and effort are better spent writing a manuscript or generating more data . unlike graduate students , there is a strong incentive for undergraduate students to make contributions to a wiki - style cir mod : they want to earn a good grade in class .
they are not yet experts in the model system or the process of annotation , however , and so their contributions vary in quality .
this is apparent in the recent contributions from our 2011 bioinformatics class ; some provide real insight into the annotation of an orf , but others add little information . any database built on wiki principles relies on user contributions to be accurate and thorough . if xanthusbase is to succeed , we must continue working toward a sustainable community - driven model . in this way
having expanded to other model organisms and research communities with openmods , we will try to learn from each other over the next 5 years .
we plan to create openmods installations for new model organisms , and to support organisms with multiple chromosomes and also chromosomes that are not circular .
one pi ( s. crosson , personal communication ) has requested that we allow changing the coordinates of orfs and also removing and adding orfs .
we will also introduce a feature that allows users of an openmods installation to vote on the importance of an annotation ( similar to the voting in stackoverflow.com ) , and show records of users by the number of votes they have accumulated .
we plan to work with the debian open source community to make the openmods package available in the debian repositories .
this will make installation easier , and we will be able to push updates to openmods installations automatically , allowing us to more easily implement new community feature requests and respond to security defects that require patches .
this will allow us to more readily accept contributions from open source developers because it will allow us to ensure that contributions from unknown developers are of sufficiently high quality .
we are seeking other pi s outside of our current set to incorporate openmods into their curriculum .
moreover , we envision a collaborative environment among each model organism s group where the community will act as ad hoc referees for the undergraduate contributions .
this will not only ensure that high - quality contributions become fixed in the database , but will teach necessary skills to the next generation of life scientists .
the benefits of introducing substantive research projects into the classroom are real ( 17 ) .
undergraduate involvement in research can improve retention in the sciences ( 18 ) and the pursuit of a graduate degree ( 19 ) . in a 2004 study of 1135 undergraduates from 41 universities
, 91% of students reported that their research experience sustained or increased their interest in attending graduate school ( 20 ) . based on our experience with the success and continued challenges of openmods
funding for open access charge : national science foundation ( mcb-0746066 , to r.d.w ) .
 xanthusbase ( http://www.xanthusbase.org ) , a model organism database for the bacterium myxococcus xanthus , functions as a collaborative information repository based on wikipedia principles . 
 it was created more than 5 years ago to serve as a cost - effective reference database for m. xanthus researchers , an education tool for undergraduate students to learn about genome annotation , and a means for the community of researchers to collaboratively improve their organism s annotation . 
 we have achieved several goals and are seeking creative solutions to ongoing challenges . along the way we have made several important improvements to xanthusbase related to stability , security and usability . 
 most importantly , we have designed and implemented an installer that enables other microbial model organism communities to use it as a mod . 
 this version , called openmods , has already been used to create xenorhabdusbase ( http://xenorhabdusbase.bact.wisc.edu ) , caulobacterbase ( http://caulobacterbase.bsd.uchicago.edu ) and soon bdellovibriobase . 
BACKGROUND: XANTHUSBASE AS A WIKI-STYLE COLLABORATIVE INFORMATION REPOSITORY
FIVE-YEAR UPDATE
ADDRESSING PROBLEM 1: O
ADDRESSING PROBLEM 2: O
ADDRESSING PROBLEM 3: O
CONCLUSIONS: O
SUPPLEMENTARY DATA
FUNDING