User manual
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1. J 7 ola ea x LINE eo oe oe ILL LL ILI lt Synchronized LJ Z To add a heat shock treatment you must specify the medium used the temperature and the age exposed You must specify an exposure time too and general comments about this treatment can be noted Into the last field As always additional media can be add with the user option menu Settings gt Add Information Once you have entered the relevant condition parameters when you click Save the treatment 1s associated with each of the strains that you had previously selected 3 D 2 8 Copy and delete a treatment When you have added a treatment by clicking on the icon for editing a condition you will see two buttons iL to copy this treatment for the selected strain x to delete this treatment Conditions x Genotype C eleganswildtype LabID N2 CGC ID not specified edit this condition Genotype C eleganswildtype LabID N2 CGCID notspecified Conditions a edit this condition ICeE User manual Page 21 28 3 D 3 Results On this page you have the possibility to associate the results of an experiment with the experimental conditions that you defined You can add one or more results files for each experiment Save this step The file format 1s not restricted so you can add any type of file such as text doc txt odt etc spreadsheets xls sxc ods etc or pictures pg png etc To add2. To edit one of your experiments you have to click on the icon for the experiment you want to edit All the information of this experiment is uploaded in the insert function and you can change the information you want This is also the starting point for duplicating a complete set of experimental conditions e g for replicate experiments see Section F3 1 for more details All versions of stored experiments are kept If you remove a file when you edit an experiment this file will be still available in the original non edited version of the experiment see Search section to know how to display a non edited version of an experiment ICeE User manual Page 23 28 Under Linux all the files of an edited version will be linked with a symbolic link to the old one Thus no additional space on the disk is required and the deletion of the link will not delete the file 3 G Search an experiment On the top left side under the name of the person who is logged in there is a search menu You can specify keywords and choose options by clicking on the buttons to configure the search function Once the search has been performed the results will be displayed on the right side 3 G 1 Search function Logout Search Settings Credits Report bug e Is20 drag 1 RNAi Sorter 2009 07 24 Olivier Zugasti ENSE You can copy redistribute and modity it See the copying file for mare When you click on the Go button these user defined words
3. RC2 Database settings Database host iocalhost Database name dml icee Database username elegans Database password Perform a Database Backup Restore a Database from a Backup Manage Dump Files Connect english v Go back to script start ICeE User manual Page 26 28 If there 1s a login error first make you sure that all the information e g password you entered is correct xt dump doesn t tell you what the problem is If you login successfully you will be taken to this screen Xt Dump v1 RC2 m Please select table s you want to backup m Backup Options C Table name V Save Structure age exposed V Save Data array Add DROP TABLE _ author Add IF NOT EXISTS author information J lt lt Use Gzip compression method cgc_strain chemical exposure Backup Filename without extention cone dump ciml icee 20140615 clone source compound Start dump procedure conditions construct construct method control experiment experiment type gene heatshock icee database version infection Here you can specify the options for the backup On the left you can choose the tables you want to save Select Table Name on the top to check all the tables On the right if you don t understand the options just accept the default choice shown in the screenshot You can define the name of the file that
4. a file all you have to do is select your file with the browse button and then click on Upload The file is then uploaded onto zu the server and it appears In the table You can delete a EE previously uploaded file by clicking on the del icon ee ee icu oid ignique a a Some characters may be replaced automatically accents spaces 2 p 3 D 4 Comments On this page you can add comments to the experiment 500 characters max General comments on the experiment ICeE User manual Page 22 28 3 E Insert the experiment Once you have filled up the relevant rubrics you will arrive at a summary page Clicking on the button of a condition will provide you with more information about each treatment You cannot edit the strain or the treatments here you have to go back to the condition page to make changes see next Section To delete a file or add one more file you have to go to the specific page results When all the details of a given experiment have been added you can insert the experiment in the ICeE database by clicking on Save in ICeE The experiment is then inserted and indexed so you can find it using the search function Genotype C eleganswildtype LabID N2 CGC ID not specified 3 oa Results files result file doc result file pdf Save in ICeE N 3 F Edit an experiment i You can edit your experiment You cannot edit other users experiments
5. have multiple conditions A condition is composed of a strain and what was done to it the treatment Accordingly this page is divided in two parts 3 D 2 1 Strain choice By clicking on add a strain a panel appears giving you the opportunity to define strains used in the experiment Most experiments will use strains that were obtained from the CGC or are part of a lab specific strain collection ICeE comes pre loaded with a complete strain CGC list see Section B 2 1 4 for updating it Lab strain lists can be added simply see also Section B 2 1 4 A strain can be chosen either using its genotype or using the strain name If you search by genotype ICeE looks in both lab strains and the entire CGC list If the strain 1s at the CGC then the Laboratory ID is automatically the same as the CGC ID For a strain that comes from the lab s list of strains but has not been sent to the CGC the CGC ID will automatically be not specified Choose strain From yours favourites By Laboratory ID 16267 By CGC ID not specified x Strain Report LL strains list The first characters entered in one of the three fields will be auto completed Then once you click on the desired strain all other fields will be auto completed too This allows you to ICeE User manual Page 15 28 check that you ve entered the right strain As an alternative you can use the drop down menu containing your favourite strain
6. precise you can enter a number in the second field green in the figure For the second field you can choose between hours minutes and seconds This unit has to be smaller than the first one Exposure Time Hour s v Minute s v 3 D 2 2 2 Specify an age exposed For every treatment you also have to specify the age at which the worms were first exposed to this treatment You can choose common stages L1 L2 L3 L4 Young adult and adult but you can also specify an age between two of those stages e g L2 L3 ICeE User manual Page 17 28 If the experiment did not involve synchronized worms uncheck the box labelled synchronized 3 D 2 2 5 Specify comments You can add general comments for every single treatment If something seems to be important to the understanding of the treatment e g it has to be started in the morning and cannot be added with the default fields you can specify it in the comments After this shared part the different default treatments have specific features and are described one by one below 3 D 2 3 Add an RNAi treatment Search RNAi Show 10 v clones a el for screen Exposure Time c Hate va Age exposed v Synchronized E 3 D 2 3 1 By clone Search RNAi pc Show 10 v clones HT115 ptc 1 Custom ptc 1 RNAI suppressed Is7 show upregulation of nlp 29 Lab In some animal sjj F21H12 4 affected gene name differs from clone name J I Ahringer m J
7. strain genotype The Laboratory ID or CGC ID is copied to the Strains list box You can add as many strains as you want Once you have finished entering strains click Save and all the strains in the list will be add to the experiment automatically Choose strain From yours favourites wt fris7 pnip 29 GFP pcol 12 DsRed IV Y By strain genotype wt fris7 pnip 29 GFP pcol 12 DsRedjIV 2 By Laboratory ID G267 By CGC ID nct specified Strain Report cf Save ICeE User manual Page 16 28 3 D 2 2 Add a treatment You can specify the treatment used on the different strains in the experiment First choose the strain s to which you want to add the new treatment by checking the box in the top left corner of desired strain s As an example Genotype C eleg The treatment will be added to this condition Genotype C brig U but not to this one Then by clicking on Add a treatment 6 icons representing the default treatments in ICeE will be shown N e N MM M N M Add a treatment Before describing the treatment specific parameters the common ones for all the treatments will be outlined 3 D 2 2 1 Specify a exposure time For all treatments you have to specify the exposure time You must specify a number in the first field red in the figure and its associated unit For the first field you have the choice between days hours and minutes If you wish to be more
8. the default settings have been designed for use in the Ewbank lab and as such reflect the type of experiments that we do but they are all easily modifiable so that we hope ICeE will be generally useful to any C elegans lab The next section of this manual concerns installation and configuration of the database Most users can skip directly to Section 2 ICeE User manual July 2014 Page 4 28 1 Installation I A Server and interface installation This part requires some basic knowledge of server configuration and access to a server where you have administrator rights Installation is straightforward but if the following section is unintelligible for you ask for help from your IT support team or nearest friendly computer scientist First of all you will need a server architecture If you don t have access to this the easiest is to download a WAMP architecture for a Windows server build a LAMP architecture for Linux server or download a MAMP architecture for Mac server Download WAMP http www wampserver com download php Install LAMP http lamphowto com Download MAMP http www mamp info en downloads index html Then download the correct ICeE archive zip or tar gz from http sourceforge net projects icee and uncompress it into the server s default web accessible directory 1 B Database installation If you installed WAMP MAMP or LAMP this will have included an installation of MySQL You wil
9. will be searched in every field in the database and experiments containing those words will be displayed on the right side 3 G 1 1 More options Here you can configure the search function for a more effective search You can search for precisely the specified word by selecting Exactly this word or a word or a sentence containing this word by selecting A word containing this word by default In the latter case rap would return entries with trap 66 99 66 wrap wrapper trapper etc By default the function searches mn all areas but with the drop down menu you can choose to search only in a specific area ICeE User manual Page 24 28 3 G 2 Results display The search function displays results on the right side in a table with experiment name experiment type the date of experiment experiment author and numbers of results files For each experiment you have two choices By clicking on the icon on the left you will see all the detail of the experiment By clicking on the icon on the right you will be able to edit an experiment if you are the author of that experiment ZRNE 3 G 3 View experiment details In results table if you click on the icon beside the experiment name you can access all the details of this experiment Non edited version 2 Non edited version 1 Non edited version 0 Then you can see the results files which can be opened or saved Lastly you ca
10. Additionally with alterations in gene prediction the supposed target s of a given clone can change For this reason the information associated with any clone can be altered To update clones when logged in as administrator click on Update clones in the settings menu under the Manage database icon You have the choice of updating the Ahringer and Vidal libraries or your own lab collection using a tab delimited text file The updating interface 1s flexible with pull down menus allowing you to choose which fields are to be included and in which order For example one can include both the primer sequences used and the predicted target gene s An example of a relatively minimal entry for a single clone would be to select in order the fields Clone name Target gene and Comments then upload a tab delimited text file Lab F26F12 5 mdc 3 sequence verified 09 02 04 Note if uploading multiple clones as a single file individual fields e g comments can be left blank if there is no information for certain clones ICeE User manual July 2014 Page 9 28 2 General description ICeE is a web based program for the storage of details of how an experiment using C elegans was performed for the storage of the corresponding results and for subsequent consultation of these results All the pages have a similar format 1 Below the ICeE banner in addition to the Logout Credits Help and Report bug bu
11. G 4 MAJOR TIME SAVER INSERT SIMILAR EXPERIMENT 25 3 H REPORTA BUG 26 3 BACKUP ICEE 26 3 1 1 DATABASE DUMP 26 3 1 2 RESULT FILES BACKUP 27 3 J RESTORING ICEE 28 ICeE User manual July 2014 Page 3 28 Introduction Many different experimental approaches generate results In the form of electronic files such as digital images or numerical data in spreadsheets In a typical laboratory setting these files are generated on machines shared by multiple users and then transferred to individual s computers for analysis and storage An individual researcher can quickly accumulate a substantial number of data files In the absence of a rational and simple method to organize files allowing the simultaneous storage of details of the biological sample and experimental protocol data can easily be misplaced or become un interpretable This situation 1s particularly acute for users of the COPAS Biosort This specialized flow cytometer is conceived for high throughput analysis sorting and dispensing of C elegans With its Reflex attachment it can analyze samples from 96 well plates With its shortest analysis cycle more than twenty 96 well plates can be handled per day Keeping track of this number of results is not a trivial task and incited us to design and implement ICeE a database coupled with a web interface to ensure that relevant information could be entered in a user friendly way and result files stored in a simple manner Many of
12. INTERFACE FOR CAENORHABDITIS ELEGANS EXPERIMENTS User manual ICeE User manual July 2014 Page 1 28 User manual Interface for Caenorhabditis elegans Experiments Version 2 Designed and produced by Fr d ric Montanana Sanchis Version 2 x Updates by Laurent Tichit ICeE version 1 X designed and produced by Renaud JULIEN ICeE version beta designed and produced by Renaud JULIEN Eric VERCHERAT Frederic GARCIA Based on work by Juliette HAYER Mathilde PELLERIN Thierry MOLINA Supervised in part by Lisa MATTHEWS Laurent TICHIT Consultant Philippe VAGLIO Conception Supervision and Project manager Jonathan EWBANK Ciml g IMMUNOLOGY Aix Marseille universit nm Inserm Contact ewbank ciml univ mrs fr ICeE User manual July 2014 Page 2 28 Contents INTRODUCTION 4 1 INSTALLATION 5 1 4 SERVER AND INTERFACE INSTALLATION 5 1 B DATABASE INSTALLATION 5 1 B 1 UPDATE STRAINS 7 1 B 2 UPDATE RNAI CLONES 9 2 GENERAL DESCRIPTION 10 3 DETAILED DESCRIPTION 11 3 A LOGIN PAGE 11 3 A 1 REGISTRATION 11 3 A 2 LOGIN 11 3 A 3 PASSWORD RETRIEVAL 12 3 A 4 LOGOUT 12 3 B HOME PAGE 12 3 C USER S SETTINGS 13 3 D INSERT EXPERIMENT 14 3 D 1 EXPERIMENT DETAILS 14 3 D 2 CONDITIONS 15 3 D 3 RESULTS 22 3 D 4 COMMENTS 22 3 E INSERT THE EXPERIMENT 23 3 F EDIT AN EXPERIMENT 23 3 G SEARCH AN EXPERIMENT 24 3 G 1 SEARCH FUNCTION 24 3 G 2 RESULTS DISPLAY 25 3 G 3 VIEW EXPERIMENT DETAILS 25 3
13. Time Hour s Y Y Age exposed v Synchronized T D You must specify the compound s concentration in the corresponding field and the unit used for specifying this concentration You must specify the age of the worms at the start of the exposure and the exposure time Then you can add comments to this treatment If you wish to add a compound medium or unit use the Settings gt Add Information dialogue boxes ICeE User manual Page 19 28 3 D 2 5 Add an infection On this page you can specify parameters for the infection ej j U Pathogen pathogen v Pathogen strain pathogen strain v Exposure Time Hour s Y CH N N N N Age exposed EN cias ll You need to specify the age of the worms at the start of the infection and the length of infection Then you can add comments to this treatment Use the Settings gt Add Information dialogue boxes to add pathogens not in the list 3 D 2 6 Add an injury On this page you can specify parameters for an injury JOJU O ej LS JU JUL 2 Injury method injury method v Age exposed Y d The default methods are pricking and laser induced Other methods can be added in the user option menu Settings gt Add Information You must also specify the age when injured Then you can add comments to this treatment ICeE User manual Page 20 28 3 D 2 7 Add a heat shock JU UA medium v C Hows
14. al abnormal dauers under exhausted conditions Strain Species Genotype Description lt Back Next Finish Cancel Text Import Wizard Step 2 of 3 This screen lets you set the delimiters your data contains You can see how your text is affected in the preview below Delimiters _ Treat consecutive delimiters as one Tab _ Semicolon Comma Text qualifier A Space V Other Data preview Strain Species Genotype Description Occasional abnormal intestine Class allele gonad daquers under exhausted conditions Cancel lt Back Next gt Finish Then the relevant information can be extracted simply by using the function Data gt Filter gt Autofilter Custom and defining the parameters as below n es gophstr ey omi pur dr ee l Ec I uy E l F L pr s 1 Straif AAL El r a Species Caenorhabditis elegans L Genotype daf 12 rh257 X 4 Description daf d Strong heterochronic phenotypes in seam somatic 8 gonad intestine Class I allele Occasional abnormal 6 dauers under exhausted conditions iit Mutagen EMS 8 Outcrossec x 9 Reference CGC 3064 Antebi A Culotti Ja Hedgecock EM 10 daf 12 regulates d e pry S in Caer Custom AuroFilter 12 De 1191 1205 19 A3 Made by Adam Antebi Sho 14 Received 10 23 00 from ms H af W I MAGN EL NEL VE T 16 Strain AAG 17 Species Caenorhabditis ual Ee St
15. first click on Add in the top navigation bar You will see Search Settings Credits Report bug D 2011 02 03 Experimenter Frederic Montanana Save this step On the left side below the name of the person logged in there are buttons that allow direct access to the different steps On the right side different fields and buttons allow one to enter the relevant information When you have completed a page you can click on Save this step to save the current data 3 D 1 Experiment details On the first page Experiment Details you must specify the experiment name the experiment type and the date the O experiment was performed You can Experimenter Frederic Montanana select an experiment type already in the database in the corresponding drop down menu to add a new experiment type go to user options and click on add information see 3 C 5 above Add the date by clicking on the input window and then choosing the date on the calendar or using the format YYYY MM DD Then click on the button Save The newly entered data is then checked and an error message will notify you of any problem with data entry Otherwise you ll be redirected to the next page ICeE User manual July 2014 Page 14 28 3 D 2 Conditions Logout Search Settings Credits Report bug Experimenter Frederic Montanana Conditions Add a strain Add a treatment Save this step An experiment can
16. h a text editor The top lines should look like this hostname WW user wn pass n base DI Enter the different fields a typical set of default values would be hostname localhost user root wn pass base ciml icee ICeE User manual July 2014 Page 6 28 Don t forget to save the edited file Now you can use ICeE with your web browser by typing this address in the address bar http your server ip address ICeE At this stage there is one default user administrator with the password elegans If you are concerned about users accessing the database management tools see Section C you should change this password ICeE comes pre loaded with a strain list from the CGC Before other users access ICeE you may want to update this to have the latest version and also incorporate your own lab s list of worm strains see next Section 2 1 4 and RNAi clones see Section 2 1 5 1 B 1 Update strains ICeE comes loaded with a recent list of all CGC strains The database administrator has the possibility of additionally entering into the database a list of strains for example from the lab s own strain collection Before doing this you should check that you have the most up to date CGC strain list The CGC currently maintains a list at http biosci umn edu CGC strains under the rubric Strain list one big text file Login as administrator c
17. is created By clicking on Start dump procedure the script will begin to save the database Do save it somewhere secure Xt Dump v1 RC2 cgc strain Saving Data 1500 0 085 E 3 1 2 Result files backup To complete a total backup of ICeE you need to save all the files present in the result file directory For that copy the entire directory ICeE uploads experiments ICeE User manual Page 27 28 3 J Restoring ICeE To restore ICeE we assume that you have made a backup of ICeE as described above Copy the database backup file into the directory ICeE xt dump dumps Then go to the ICeE user settings and click on manage database Then select Make a database backup restore the database or manage the backup files You will be redirected to the XT dump interface Enter the database host by default this is localhost then the ICeE database name ciml icee by default Then enter your MySQL username and the password to connect the database Choose the option Restore a Database from a Backup and hit Connect If you have copied the database backup file correctly you can choose it from the drop down menu Hit Start Restore To complete the restoration just copy and paste the ICeE result files directory in the same place If all goes as 1t should you will have restored a version identical to the one that you had backed up ICeE User manual Page 28 28
18. k on Update lab strains in the settings menu under the Manage database icon then select your file with the browse button and then click on Update If you subsequently need to update your lab strain list having first updated the CGC list see above you can either enter a list of just the new strains or submit your entire updated strain list In this case ICeE adds any new strains and by default checks for modifications to existing strains 1 e change in genotype and modifies the relevant entries If you don t want to upload the entire list of CGC strains it 1s relatively simple to convert the CGC s Strain list one big text file to a suitable format for import For example the file can be imported into Excel as colon delimited text Text Import Wizard Step 1 of 3 The Text Wizard has determined that your data is Fixed Width If this is correct choose Next or choose the Data Type that best describes your data Original data type Choose the file type that best describes your data Delimited Characters such as commas or tabs separate each field _ Fixed width Fields are aligned in columns with spaces between each field Start import at row 3 File origin Macintosi Preview of file Macintosh HD Users ewbank Data Wor gophstrnt txt D I Caenorhabdi tis elegans daf 12 rh257 X daf d Strong heterochronic phenotupes in seam somatic gonad intestine Class allele Occasion
19. l have had the possibility of adding users and passwords and defining access rights In this case or if you are installing ICeE on a server that already has been configured with a web browser go to http your server ip address ICeE xt dump or http localhost ICeE xt dump if you have installed it on your own computer Enter the database host by default this is localhost then the database name You need to choose a database already installed on MySQL Server by default MySQL installs one called mysql Normally you should use this Then enter your MySQL username and the password to connect the database Then choose the option Restore a database from a backup and hit Connect If there is a login error first make you sure that all the information e g password you entered is correct xt_dump doesn t tell you what the problem is ICeE User manual July 2014 Page 5 28 Xt Dump wi RC Database settings Gate Daabasu sasan Database username Ee Perform a Database Backup F Restore a Database from a Backup jat Manage Dump Files Go back to script start Xt Dump vi RC2 http www dreaxteam net Check Then select the only file available ICeE install sgl and click on Start Restore Xt Dump v1 RC2 Please select the file Go back to script start Xt Dump vi RC2 http www dreaxteam net Check new version Once the database is installed open the file ICeE php includes db config php wit
20. lick on Update CGC strains in the Settings menu under the Manage database icon enter http www cbs umn edu sites default files public files celelist2 txt and then click on Update It is possible that in the future the CGC will change the name or location of this file check with them if it Is no longer obvious where to find it This process can take quite some time if the list has not been updated regularly When it has finished you should see the message Update finished with success with a link to a text file listing the names of the added strains Once you have the CGC strain list you are ready to enter your lab strain list The file must be in a standard simple format If for example you use Excel just save the two columns as tab delimited text or if you use FileMaker M use Export records again as tab delimited text The output should look like this IGI unc 32 e189 ced 7 n1892 IIL ced 5 n1812 dpy 20 e1282 IV IG2 wGfrExI pRFA set 1p GFP IG3 wGfrEx2 pRFA set 1p GFP IG4 wt oxExl66 phsp transposase unc 122p GFP oxEx229 Mos1 myo 2p GFP IG6 smf l eh5 X IG7 wt frEx4 pRF4 pStol 1 GFP IG8 wt frEx5 pRFA pStol 1 GFP Note that some applications might include manual line breaks symbol Remove these e g in Microsoft Word use replace 11 is the code for before uploading your file ICeE User manual July 2014 Page 7 28 Once you have your file clic
21. n see details of all conditions and all treatments of this experiment in a summary display To see more about each treatment in a condition you can click on 3 G 4 Major time saver Insert similar experiment ICeE User manual Page 25 28 3 H Report a bug In ICeE you can directly report a bug on sourceforge This will notify the developers of ICeE Click on Report Bug in the navigation bar You will be redirected to Sourceforge Here you can submit your bug aka Artifact Please try to be as precise as possible Add Artifact Project ICeE Private Category None v Group None Y 3 1 Backup ICeE If you want to save all the data entered In ICeE you have to do two steps 3 1 1 Database dump First of all you need to save the information entered in the database and the structure of the database To do this go to the ICeE user settings and click on manage database Then select Make a database backup restore the database or manage the backup files You will be redirected to the XT dump interface Depending on your system you may see a few lines of error messages at the top of the page This should not interfere with the backup process Enter the database host by default this is localhost then the ICeE database name ciml icee by default Then enter your MySQL username and the password to connect to the database Choose the option Perform a Database Backup and hit Connect Xt Dump v1
22. r Be aware that when you log out all data not saved in the database will be lost But in all cases you are recommended to logout at the end of each session to avoid any potential problems 3 B Home page Logout Search Settings Credits Report bug Add Q search L E EEN NN A E s EE SE EES Jick ont gt Icon ex I 2a scr20 12 10 Crib Is7 Dc L1 2010 1220 Jerome Belougne EXES scr22 11 10 Crib Is7 Dc L1 2010 11 22 Jerome Belougne Test ont Jens eegenen o 3 On this page you will see the recent activity in ICeE The upper panel 1s a summary of the last five experiments inserted in the database The lower panel lists the last five experiments you inserted In these tables if you click on the icon beside the experiment name you will see the details of the experiment From this page you can also insert a new experiment with the Add button or query the database with the Search button These functions are explained below ICeE User manual July 2014 Page 12 28 PD Add Q search 3 C User s settings In the navigation bar you can access the user s settings Here each icon allows you to modify pre existing data or add information to ICeE From left to right 1 2 3 4 5 The password here you will be able to modify your password once you have specified the old one The secret question and answer here you will be able to modify your secret question and answe
23. r once you have specified your password Manage datatabase These options are only available to the administrator Here you can access the XT Dump interface to save or restore your database see Section 3 H for more information update your strain or clone library see sections 1 B 1 and 2 or go to Sourceforge to check for a new ICeE version Favourite strains here you can add a strain that is already in the list of strains in the ICeE database to your personal set of favourite strains to allow you a quicker access to them when adding a new experiment Add information this part allows you to add to the elements available for the description of a new experiment If the default values in ICeE are not appropriate for the description of your experiments you can add some elements here including the type of the experiment or the concentration units The choice is relatively broad If ever you need to make more extensive changes to the structure of the database as ICeE is open source you or a savvy colleague can modify the code The ICeE developers have moved on in their professional lives and unfortunately cannot customize ICeE for you ICeE User manual July 2014 Page 13 28 3 D Insert experiment Important tip Once you begin to fill in fields in this part of ICeE the information is not kept if you logout or close your web browser It will only be entered into the database when you hit Save To insert an experiment
24. rain e 18 Genotype daf 12 rh34 X 19 Description daf d Strong 20 gonad intestine D 21 Mutagen EMS Gg 22 Outcrossec x2 uas Genotype i 23 Reference CGC 3064 A 24 daf 12 regulates d 25 alternative in Caer 26 De 1191 1205 199 Use to epr santa Die characte 27 Made by Ed Hedgecock 28 Received 10 23 00 from 5 to represent any senes of haass 29 30 Strain AALO 31 Species Caenorhabditis Cancel DK 32 Genotype daf 12 rh286 33 Description Weak heteroch ICeE User manual July 2014 Page 8 28 The resulting table can be saved as a tab delimited text and using a replace function it can be turned into the right format AA daf 12 rh257 X AA6 daf I2 rh84 X AA10 daf 12 rh286 X AA18 daf 12 rh61rh412 X AA34 daf 12 rh61 X AA82 daf 12 rh284 X AAS83 daf 12 rh62rh157 X AAS85 daf 12 rh285 X AAS89 daf 12 rh274 X AA107nhr 48 0k178 X Once the desired lists are ready they can be uploaded 1 B 2 Update RNAi clones ICeE also comes pre loaded with the list of RNAI clones from the original Ahringer and Vidal libraries We have included tentative lists of target genes based on information from Wormbase W 8210 but users should be aware that the attribution of targets 1s not reliable as for example Wormbase does not take into consideration the fact that Vidal clones are generated from cDNAs unlike the genomic Ahringer clones
25. s see Section 3 C 5 By choosing one strain from this list all the fields will be filled with the information available for this strain If you choose a strain that is in Wormbase clicking on Strain Report will open a new page tab with the relevant page at Wormbase Note as Wormbase does sometimes change its database structure and so URLs change this feature might not work in the future Experiments generally fall into two types one in which a single strain 1s subject to multiple experimental treatments and secondly experiments that involves multiple strains At this step you therefore have two choices 3 D 2 1 1 Experiment with a single strain Once you have chosen the right strain by clicking Save the strain will be added to the experiment immediately Then 3 icons appear Conditions Genotype wt fris7 pnlp 29 GFP pcol 12 DsRed IV Lab ID IG267 CGC ID not specified x x D allows you to copy the strain and any treatment associated with it 1 allows you to edit the strain used and to show the details of any treatment associated b y y with it allows you to delete the strain and any treatment associated with it 3 D 2 1 2 Add a strain list If on the other hand your experiment involves more than one strain you can make a list of all the strains you used in the experiment and add all of them at one time To add a strain to the list just click the button on the right of the input By
26. tanana Password MC JJ Please enter your username or create a new account Register The first page 1s a login page On this page you can register to create a new account or log in by entering your username and your password 3 A 1 Registration If you are not registered click on the button EI You will be directed to the register page where you can type a new username as well as password secret question and secret answer The secret question and answer will be used if ever you forget your password so do pick something that is simple and obvious for you When you click on the register button this new username will be inserted in the database and you ll be redirected back to the login page where you can now log in 3 A 2 Login When you type the first letters of your username if you are registered your name will be auto completed Usemame o Frederic Password montanana Logn J ICeE User manual July 2014 Page 11 28 3 4 3 Password retrieval If you have forgotten your password or enter an incorrect password the message below will appear If you do hit here you will be asked the secret question that you defined when you registered If you give exactly the right answer your old password will be replaced by the password elegans You should change this as soon as you log in again 3 A 4 Logout Your session will not end until you logout or quit your web browse
27. ttons which are self explanatory the four other buttons allow access to the different parts of the interface 2 This is the main display part of ICeE Here you will be able to input information about experiments as in the screenshot below or see the results of databases searches 3 The sidebar displays the different steps you use when you add an experiment as in the screenshot or the options when you go to the search page Logout Search Settings Credits Report bug Sate I A 2 f Enter the name of the experiment r Ge Date 2011 02 02 Experimenter Frederic Montanana Save this step Sometimes you will see different type of messages in ICeE 1 Success message K RR This kind of message notifies you of the success of an operation 2 Information message Here the message will just notify you about something you should know 3 Warning message PERROS This message will appear when you have done something wrong or you have forgotten something 4 Error message We hope you won t see this type of message as it means that there is something preventing ICeE from running normally Please send the message to your administrator ICeE User manual July 2014 Page 10 28 3 Detailed description 3 A Login page Enter ICeE b Search Settings Credits Report bug Welcome to the Interface for Caenorhabditis elegans Experiments Username Frederic Mon
28. ulie ICeE User manual Page 18 28 On the top you can look for a clone using a text search Every clone name containing this text as well as every clone targeting a gene containing this text will be shown If required you can change the maximum number of results displayed the default is 10 If the clone you used is not in the list then it will need to be added see Section Section B 2 1 5 For the chosen clone you must specify the age of the worms at the start of the exposure and the exposure time Then you can add comments to this treatment 3 D 2 3 2 By plate Input a plate list specific for screen 3 plates There is another way to specify clones used in an RNAi experiment using this area to add plates of RNAi clones For example in a screen it might be that multiple 96 wells plates with a different RNAi clone in each well are treated in parallel on the same day and it is reasonable to consider this as a single experiment This field is not restricted in any way You just have to add one plate per line The best 1s obviously to use an ID that refers to a list or database describing in detail the contents of each plate For all the plates you must specify the age of the worms at the start of the exposure and the exposure time Then you can add comments to this treatment 3 D 2 4 Add a chemical treatment d konee QUO Quy qv ese Compound compound v Medium medium Y Concentration unt Y Exposure
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