Hanna Pincas. Sealfon Laboratory, Department of Neurology, Mount Sinai School of Medicine, New York, NY. Created 01/06/2009. Revised 01/13/2011

Transcription

1 Tutrial fr the Cntur Electrnic Lab Ntebk (CnturELN) sftware Hanna Pincas Sealfn Labratry, Department f Neurlgy, Munt Sinai Schl f Medicine, New Yrk, NY Created 01/06/2009 Revised 01/13/2011 Cntact infrmatin: hanna.pincas@mssm.edu Tel.: Ext.: r

2 Cntents I. Main features f CnturELN 2 II. Getting Started 3 Navigatin Tls 3 i. My lab ntebk Navigatr 4 ii. Library Navigatr 4 iii. Template Navigatr 5 iv. Search Navigatr 9 III. Creating a New Experiment 10 IV. Clning, Sharing, and Submitting an Experiment 11 i. Clning an Experiment 11 ii. Sharing an Experiment 11 iii. Submitting an Experiment 12 I. Main features f CnturELN CnturELN is a sftware suite that enables investigatrs t rganize their experimental data in an efficient and secure way. The wrkspace is user-friendly and supprts mst data frmats, frm Excel spreadsheets t PDF images, r any type f File attachments. Users may create an Experiment using an apprpriate Experiment Template, which significantly saves time and increases dcumentatin clarity and quality. Users may clne an Experiment, in case they carry ut analgus experiments, e.g. experiment duplicates r triplicates. Users may share an Experiment: users may chse t share an Experiment they are bth invlved in, and thereby add data/infrmatin t it. Users may submit an Experiment: users shuld submit an Experiment ONLY nce it is cmpleted, in rder t lck up the data. This means that all the data/infrmatin entered can n lnger be edited. Users can view the Lab ntebks f ther Users frm the same grup (e.g. Sealfn lab). Thus, knwledge sharing and cllabratin are prmted in the benefit f research prgress. Users can search fr Experiments by using key wrds r ther criteria f their chice. 2

3 II. Getting started Duble-click n the CnturELN icn lcated n yur cmputer desktp a CnturELN Lgin windw pps up. Type in User Name and Passwrd, then click OK. the User s lab ntebk Navigatr page pens up: Navigatin Tls Underneath the Menu bar, there are 4 icns symblizing 4 Navigatin Tls (i-iv). The User may click n the icns t navigate thrugh thse Navigatin Tls: 3

4 i. My lab ntebk Navigatr Displays a summary f the User s lab ntebk (see image abve) T view a cmplete list f the User s experiments, click n View cntents f the entire ntebk ii. Library Navigatr Displays: - a list f all Persnal lab ntebks in alphabetical rder by User s Last Name click n a User Name t view his/her list f Experiments - a list f Prject lab ntebks in alphabetical rder by Prject name click n a Prject name t view a list f Experiments that belng t that Prject!! Nte that a list f Experiments can be srted by: Experiment n. Experiment Name Prject (t which Experiments belng) Authr f the Experiment 4

5 Date f Creatin Date f Last Edit Size f the Experiment (in kb) Experiment Type (r Assay type) iii. Template Navigatr a/ View cntents f the Public Templates flder by clicking n it displays a list f all Experiment Templates (18) available t the User: BRET/FRET Cell Line Preparatin Cell Preparatin ChIP Assay Flw Cytmetry IHC & ISH Imaging Flw Cytmetry Luciferase Assay Manuscript Experiment Master in vitr Experiment Master in viv Experiment Micrarray experiment Multiplex ELISA Receptr Binding Assay RNA Extractin RT-qPCR Virus Preparatin Western blt!! Nte that Public Templates can nly be altered by the ELN administratr. The user is strngly advised t: 1) cpy /paste Public Templates int My Templates flder using the muse right-click 2) mdify the Templates accrding t his/her needs, 3) save them fr future use by clicking n File->Save b/ View cntents f the My Templates flder by clicking n it displays a list f the User s wn Experiment Templates 5

6 c/ Experiment Templates: Rules and Examples T create a New Experiment in the ELN, the User must create: - a Master Experiment - ne r mre Sub-Experiments/Assays that are linked t the Master Experiment An Experiment is typically cmprised f several bilgical assays, therefre we designed: 2 Master Experiment Templates: Master in vitr Experiment (Fig.1), which is a Parent Experiment template specifically designed fr an in vitr study; Master in viv Experiment, which is a Parent Experiment template specifically designed fr an in viv study. 15 Sub-Experiment/Assay Templates (see example illustrated in Fig.2) 6

7 Figure 1: Illustratin f the Master in vitr Experiment Template 7

8 Figure 2: Illustratin f the Flw Cytmetry Assay Template 8

9 iv. Search Navigatr Allws t search either the User s Lab ntebk r the Entire ELN Library: - by keywrd r ther - using the Advanced ptins criteria: - by Experiment n. - by Title (i.e. Experiment Name) - by Prject - by Experiment Type 9

10 III. Creating a New Experiment!! Nte: nce an Experiment has been created, it cannt be deleted frm the User s Lab ntebk. 1. In the Menu bar, g t File -> New Experiment 2. Select Create experiment frm a template 3. Select a template categry, e.g. Public Templates 4. Select the desired template based, e.g. RT-qPCR 5. Click OK A New Experiment pens up: 6. Fill in the fllwing Sectins in New Experiment:!! Nte that fields marked by * are mandatry. Title (i.e. Experiment Name) Prject: select Prject(s) frm a Prject list by clicking n the Primary cntact (i.e. the User s address): select by clicking n the Organizatin (i.e. Institutin name): select by clicking n the Organizatin address (i.e. Institutin address): select by clicking n the Secndary cntact (i.e. ther User invlved in Experiment): select by clicking n the Secndary cntact s rle 10

11 Etc. 7. Optinal: insert additinal Sectins int New Experiment Click nce n the title f a Sectin (a) that is already present in the New Experiment Select a new Sectin (b) frm the Sectin Tlbx lcated n the left-hand side, e.g. Experiment type Duble-click n the selected Sectin (b) Sectin (b), e.g. Experiment type, is nw inserted beneath Sectin (a). Yu may select the apprpriate Experiment type by clicking n the Alternatively, yu may: Click nce n the title f a Sectin (a) that is already present in the New Experiment In the Experiment Menu bar, click n Insert -> Sectin -> Bdy Text Image Excel wrksheet PDF dcument Text field File Attachment [ ] Reference -> [ ] Experiment type [ ] Users invlved Select a new Sectin (b) amng thse listed, e.g. Experiment type Sectin (b), e.g. Experiment type, is nw inserted beneath Sectin (a). Yu may select the apprpriate Experiment type by clicking n the!! Ntes: t change the title f a Sectin, duble-click n its title and type in the crrect title. t mve a Sectin up r dwn, first select it, then mve it t the desired psitin using the yellw up/dwn arrws lcated in the Tl bar. IV. Clning, Sharing, and Submitting an Experiment i. Clning an Experiment Click n File -> Clne Experiment This creates a new Experiment that is identical t the previus ne: attached files can be deleted and replaced with new nes. ii. Sharing an Experiment Click n File -> Prperties -> Sharing -> -> Select Share this experiment Click n Update Users -> Type in User name f anther User 11

12 -> Select the User name in the Search result Bx and use arrws t select it in the Users Bx -> Click n Save and Exit Select the User name again and click OK The User nw shares his Experiment with anther User r Cntributr.!! Imprtant nte: The Cntributr can nw add a Sectin t a User s Shared Experiment, by fllwing the steps belw: Open the Shared Experiment In the Experiment Menu bar, click n File -> Edit Experiment Click n Insert -> Sectin -> Bdy Text, Image, Etc. Mve the added Sectin t the desired psitin using the yellw up/dwn arrws lcated in the Tl bar. iii. Submitting an Experiment Click n File -> Submit A padlck icn appears at the bttm left f the Experiment, indicating that data can n lnger be mdified. The User may still add an erratum f additinal data at the bttm if need be. 12