Tutorial 7: Automated SRM data analysis using mprophet
|
|
- Iris Edwards
- 5 years ago
- Views:
Transcription
1 Tutrial 7: Autmated SRM data analysis using mprphet mprphet is a statistical tl which can be emplyed t achieve autmated high-cnfidence identificatin f peptides. It has three functinalities: First, mmap cmbines the raw data (mzxml files) with the meta data prvided in the transitin input file. Secnd, mquest detects all peak grups amng the recrded transitins and scres all detected peak grups fr a number f characteristics (e.g. shape crrelatins, etc.). Third, mprphet cmbines the individual peak grup scres int a single discriminant scre (d_scre) fr ptimal recvery f true signals, while cntrlling the FDR. Decy transitin grups are used as negative cntrls. They represent peptide species that are absent frm the bilgical samples, and help t parameterise the null distributin fr estimating the sensitivity and the FDR. Finally, all detected peak grups fr each recrded transitin grup are ranked based n their discriminant scre and reprted. Nte that mprphet relies n prbabilistic mdelling. It subdivides each dataset int a training set and a test set, in rder t first train a classifier and then apply it t the whle dataset. Since a training set is chsen at randm, results frm repeated analyses f the same data may vary slightly. mprphet can use tw different types f decy transitins: Empirical decy transitin grups are included in the measurements. They can be created e.g. by adding a randm integer t the precursr and fragment in masses, respectively. The empirical decy transitin apprach is highly recmmended fr wrkflws that lack reference peptides. The disadvantage f this apprach is that the empirical decy transitin grups have t be added t the transitin list befre the SRM measurements, which increases the amunt f transitins t be measured. Synthetic decy transitin grups are derived pst-acquisitin, by shifting the retentin time f the endgenus transitin peak signals by a factr defined in the parameter file (0.5 is the recmmended value). The synthetic decy apprach is recmmended fr wrkflws that include istpe-labelled internal standards in the samples. The advantage f this apprach is that the decy transitin grups d nt have t be measured. mprphet ffers several pre-defined wrkflws, which reflect the design f the experiment and define specifics f the decy transitin apprach. In this tutrial we will apply the tw mst cmmn appraches t ur case study. Fr an verview f all wrkflws see the table at the end f this tutrial. Wrkflw SPIKE_IN + synthetic decys Parameter file: param_aqua_heavy_stringent_ref_synthetic.def Target transitins measured fr light and heavy peptides Reference peptides are heavy peptides and we assume they are always present Synthetic decy transitin grups are generated frm the data Wrkflw LABEL_FREE + empirical decys Parameter file: param_light_nref.def Target transitins measured fr light peptides N reference peptides Empirical decy transitin grups measured alng with target transitin grups 1
2 Open the mprphet virtual machine Duble click n the.vmx file t pen the mprphet virtual machine (VM) and lgin if necessary (username: mprphet, passwrd: mprphet). Enable flder sharing in the virtual machine settings Fr the VMware player (Windws) the flder sharing is dne in either f the fllwing ways, depending n the versin: Player à Manage à Virtual machine settings à Optins à Shared flders. Select Always enabled and Add the flder Tutrial- 7_mPrphet. VM à Settings à Optins à Shared flders. Select Always enabled and Add the flder Tutrial-7_mPrphet. Fr VMware Fusin (Mac) the shared flder is added under: Virtual Machine à Settings à Sharing. Turn "ON" the "Shared flders" ptin, click n the "+" buttn, brwse t the flder Tutrial-7_mPrphet and click "Add". On the VM yur shared flder can be accessed thrugh: Places à Cmputer à File Systems à mnt à hgfs à Tutrial-7_mPrphet T adjust the keybard t yur preferred language settings: System à Preferences à Keybard Flder system t brwse files Terminal / Cmmand line Ggle Chrme brwser Change keybard language Exprt transitin infrmatin frm Skyline using a custm reprt frmat On yur laptp (nt VM), pen the file SRMcurse_ _iRT.sky frm the flder Tutrial-5_Scheduling. Exprt transitins and ther relevant infrmatin in a custm reprt frmat: File à Exprt à Reprt à Imprt à Select mprphet.skyr à mquest_mrmprphet nw appears in the list. Inspect it by clicking the Preview buttn. One clumn has t be added t this new reprt: Edit list à Select mquest_mrmprphet reprt à Edit à Rename it t mquest_mrmprphet_irt and add the clumn RetentinTimeCalculatrScre à click 2x OK. Save the resulting transitin list as mprphet _ _label.csv int the flder mprphet_ _label in Tutrial-7_mPrphet. 2
3 Refrmat Skyline reprt using mgen On the VM, pen the terminal and change t the fllwing directry: cd /mnt/hgfs/tutrial-7_mprphet/mprphet_ _label Refrmat line breaks f the transitin list t UNIX frmat: Install the tfrds: sud apt-get install tfrds (pwd is mprphet ). This cmmand requires a wrking internet cnnectin. Run: frmds mprphet_ _label.csv Run mgen: mgen.pl -SKY mprphet_ _label.csv -num_decys 0 We set 0 decys, because we d nt want t generate decys here. The utput file ends with _s01_decy. On yur laptp (nt VM), pen the newly generated file in Excel and rerganise it such that nly the fllwing clumns remain (headers f the required clumns are given in brackets): 1. Precursr in mass (Q1) 2. Fragment in mass (Q3) 3. Prtein name (prtein_name) 4. Unmdified peptide sequence (stripped_sequence) 5. Precursr charge state (prec_z) 6. Istype f the peptide, e.g. heavy r light (istype) 7. Fragment in type, e.g. b- r y-in (frg_type) 8. Fragment number (frg_nr) 9. Fragment in charge state (frg_z) 10. Relative library intensity f transitins within ne transitin grup, nrmalised t 100. (relative_intensity) 11. Expected retentin time f the peptide: Rename PredictedRetentinTime t Tr_recalibrated. (Tr_recalibrated) 12. irt: Rename RetentinTimeCalculatrScre t irt (irt) 13. Decys: In the label-wrkflw n decys are needed, hence this clumn can be deleted. Otherwise enter 1 fr decys and 0 fr nn-decys. (decy) 14. Delete all ther clumns. Save as tab-delimited file: mprphet_ _label_md.txt. - On mac save as MS-DOS txt. Rename ending t.xls: mprphet_ _label_md.xls. Refrmat line breaks t UNIX: frmds mprphet_ _label_md.xls Delete the ther.csv, xls and.txt files frm the flder. Run mprphet t identify target prteins T run mprphet, make sure yu have all data files (.mzxml), the transitin list (.xls), and the parameter file (.def) in flder mprphet_ _label. On the VM, run all three functinalities f mprphet (mmap, mquest and mprphet) tgether using the minteract.pl cmmand: minteract.pl -mmap -mquest -mprphet -wrkflw SPIKE_IN - mmap_machine QTRAP -mmap_cycle_time 2 -def param_aqua_heavy_stringent_ref_synthetic.def Ntes This cmmand takes a while and might give a lt f errr messages. Please wait until it is finished befre yu click anything. Yu can mnitr the prgress by lking at the newly generated files in the flder mprphet_ _label. Fr TSQ data, the parameters -mmap_machine and - mmap_cycle_time d nt have t be defined. If yu wuld like t repeat the mprphet analysis n the same data, use the -frce ptin at the end f the minteract cmmand line t enfrce the re-analysis f files that have already been prcessed. 3
4 Tip! It is better t type these cmmands manually int the terminal rather than t cpy and paste them, t avid incmpatibilities between DOS and UNIX. Tip! T see a list f all pssible parameters fr mprphet, run: minteract.pl -manual Tip! minteract crdinates mmap, mquest and mprphet and allws a ne cmmand analysis. Hwever, the three cmpnents can als be run separately (see mprphet manual n the website fr mre infrmatin). Inspect mprphet results mprphet results are written t the flder mprphet_ _label where yu ran the cmmand. The fllwing result files are imprtant: mprphet.pdf This file cntains histgrams f all the different sub-scres and the verall discriminant scre stratified by target and decy peak grups (left figure) as well as the estimated sensitivity and errr rate fr discriminant scre cut-ffs (right figure). à Inspect the separatin between decy and target peak grups and the sensitivity (s-value) and FDR (q-value). The s-value represents the expected prprtin f true psitive peak grups dependent n the discriminant scre cut-ff and the q-value the expected prprtin f false psitives dependent n the discriminant scre cutff. The aim is t define a discriminant scre cut-ff resulting in a high sensitivity at a lw FDR. Nte that the s-value des nt reach 1 because the retentin time peptides are excluded fr the statistical mdels, but later n cunted twards the ttal. mprphet_raw_stat.xls This file prvides the discriminant scre cut-ff fr every pssible FDR. It is recmmended t select a d-scre cut-ff that crrespnds t an FDR f 1%. à In ur case, accrding t mprphet, the FDR f the cmplete dataset withut applying any cut-ff is already very lw (0.2%) and n cut-ff can be applied based n the FDR. mprphet_all_peakgrups.xls This file cntains all the peak-specific scres extracted and calculated frm the SRM traces acrss all the samples. We will need nly a few f the clumns t cntinue (see belw). shtml files These files can be pened frm within a web brwser and allw the visualisatin f all the extracted peak grups fr each SRM run (see next sectin). 4
5 Visualise the mprphet results On the VM, cpy yur data flders t the VM hme directry: cp -R /mnt/hgfs/tutrial-7_mprphet/mprphet_ _label/ //hme/mprphet/mprphet_data_analysis/ There is a space befre the //. D nt change the name f the flders anymre. On the VM, pen Ggle Chrme (link n Desktp) and navigate t yur mprphet results using the fllwing URL: Here yu can find fr each f the 9 input data files (mzxml) a crrespnding shtml file, which yu can nw pen and brwse. Click thrugh the peptides f a few samples and inspect the peak picking by lking at the plts and the scres in the table. (Decy peptides are marked by a 1 in the right clumn.) Here are a few pints that yu shuld pay attentin t: Which d-scre cut-ff is apprpriate fr the current data set? At which d-scre d the first decys appear? Fr which precursr was the wrng peak grup picked and why? Cmpare the scres and plts f the secnd and third peak grup by clicking n the peak grup rank in the table. Are there interfered transitins? Prcess mprphet results The mprphet scres fr each precursr can be fund in the file mprphet_all_peakgrups.xls. Befre cntinuing with dwnstream analysis, refine the table in Excel: Remve irt peptides and decys (decy clumn à TRUE). Remve all peak_grup_rank >1 Remve peaks with d-scre lwer than the d-scre cut-ff yu selected frm manual inspectin in the visualisatin step abve. Save as mprphet_all_peakgrups_label.xlsx. 5
6 mprphet results fr identificatin The m-scre represents the FDR f each identified peak grup. mprphet results fr quantificatin mprphet utputs als cntain all necessary infrmatin fr quantificatin. Yu can either directly extract quantitative infrmatin fr each precursr (e.g. light_heavy_rati_ttalxic) r extract quantitative infrmatin fr each transitin individually (e.g. abs_area_cde_target and abs_area_cde_ref). Dwnstream statistical analysis can be dne e.g. using the sftware SRMstats, which will be discussed in detail tmrrw. Label-free mprphet analysis Repeat the mprphet analysis fr the label-free dataset in the sub-flder mprphet_ _label-free. Start with the Skyline file SRMcurse_ _label-free_decys.sky frm the flder Tutrial-7_mPrphet which cntains a decy transitin grup fr every target transitin grup. Nte! These decys were added in Skyline thrugh Edit à Refine à Add decy peptides à 30 decy precursrs (Skyline autmatically excludes irt peptides fr decy generatin) à Decy generatin methd: Randm mass shift. We are nt generating these decys urselves in this tutrial, because randm m/z shifts are btained every time decys are generated and thus will nt fit t the acquired data anymre. Next t the m/z f each Precursr and transitin the mass shift f the decy is indicated in brackets. Exprt a reprt using the mquest_mrmprphet_irt reprt frmat: mprphet_ _label-free.csv. On the VM, in the terminal change the wrking directry: cd /mnt/hgfs/tutrial-7_mprphet/mprphet_ _label-free Cnvert line breaks t UNIX frmat: frmds mprphet_ _label-free.csv Run mgen t refrmat it: mgen.pl -SKY mprphet_ _label-free.csv -num_decys 0 Mdify the utput as described fr the label-based analysis, but remve the irt clumn and add a decy clumn which cntains 0 fr target peptides and 1 fr decys (indicated in prtein_name clumn). Save as (MS-DOS) tab-delimited file: mprphet_ _labelfree_md.txt. Rename ending t.xls: mprphet_ _label-free_md.xls. Refrmat t UNIX: frmds mprphet_ _label-free_md.xls Delete the.csv and the.txt files frm the flder. Run mprphet: 6
7 minteract.pl -mmap -mquest -mprphet -wrkflw LABEL_FREE - mmap_machine QTRAP -mmap_cycle_time 2 -def param_light_nref.def Cpy the results t the virtual machine fr visualisatin: cp -R /mnt/hgfs/tutrial-7_mprphet/mprphet_ _label-free/ //hme/mprphet/mprphet_data_analysis/ Inspect the peak picking in the shtml-files. Refine the mprphet_all_peakgrups.xls as described abve and save as mprphet_all_peakgrups_label-free.xls. Exercises 1. Which are the scres that mprphet takes int accunt fr the discriminatin f true and false peak grups fr the label-based and the label-free wrkflw, respectively? 2. What is the typical range in delta_irt f the best-scring peak grup? 3. Which d_scre cut-ff wuld yu chse t get gd results fr the label-based and label-free analysis, respectively? Which FDR and sensitivity wuld yu get accrding t the suggested cut-ff (mprphet_raw_stat.xls)? Is the FDR estimated by mprphet what yu wuld expect? Why/why nt? 4. Lk at a few examples where mprphet picked the wrng peak and try t explain why this happened. 5. Hw wuld the results change if yu used as an input fr mprphet a transitin list which has been refined befre in Skyline (i.e. cntaining nly nn-interfered transitins)? Acknwledgements and References The descriptins f this tutrial were adapted frm a manuscript which will sn be published (Surinva et al., Nature Methds 2013, in press). Many thanks t Silvia Surinva and Ruth Hüttenhain fr giving us access t the manuscript! Fr mre infrmatin check the mprphet website ( and the fllwing publicatin: Reiter, L., Rinner, O., Pictti, P., Hüttenhain, R., Beck, M., Brusniak, M.-Y., Hengartner, M.O., and Aebersld, R. (2011). mprphet: autmated data prcessing and statistical validatin fr large-scale SRM experiments. Nature Methds 8, We wuld like t thank Prime-XS and SystemsX fr supprting the. 7
8 mprphet wrkflws and assciated parameter files The fllwing table describes different experimental designs fr SRM experiments and suggests the wrkflw and parameter file required fr the mprphet analysis f SRM data derived frm the different experimental designs (Surinva et al., Nature Prtcls 2013, in press). The parameter file fr all the wrkflws can be fund in the directry /usr/lcal/apps/bignsys/mquest/cnf/ accessible via the mprphet virtual machine. Experimental design Wrkflw Parameter file Target transitins measured fr light Reference peptides are heavy. Empirical decy transitin grups measured fr light peptides. Target transitins measured fr light Reference peptides are heavy. Synthetic decy transitin grups are generated frm the data. Target transitins measured fr light Reference peptides are light. Empirical decy transitin grups measured fr heavy peptides. Target transitins measured fr light Reference peptides are light. Synthetic decy transitins generated frm the data. Target and empirical decy transitins measured nly fr light peptides. Target and empirical decy transitins measured nly fr light peptides. Target and empirical decy transitins measured fr light and heavy peptides. Reference peptides derived frm metablically heavy labeled sample (e.g. SILAC/N15). Target transitins measured fr light Reference peptides derived frm metablically heavy labeled sample (e.g. SILAC/N15). Synthetic decy transitins generated frm the data. Target and empirical decy transitins measured fr light and heavy peptides. Reference peptides derived frm a light (nn-labeled) sample. Target transitins measured fr light Reference peptides derived frm a light (nn-labeled) sample. Synthetic decy transitins generated frm the data. SPIKE_IN SPIKE_IN INVERTED_SPIKE_IN INVERTED_SPIKE_IN LABEL_FREE LABEL_FREE LABEL LABEL LABEL LABEL param_aqua_heavy_stringent_ref.def param_aqua_heavy_stringent_ref_ synthetic.def param_aqua_light_stringent_ref.def param_aqua_light_stringent_ref_ synthetic.def param_light_nref.def param_heavy_nref.def param_silac_heavy_ref.def param_silac_heavy_ref_synthetic.def param_silac_light_ref.def param_silac_light_ref_synthetic.def 8
Tutorial 3: Building a spectral library in Skyline
SRM Curse 2013 Tutrial 3 Spectral Library Tutrial 3: Building a spectral library in Skyline Spectral libraries fr SRM methd design and fr data analysis can be either directly added t a Skyline dcument
More informationTutorial 4: Parameter optimization
SRM Curse 2013 Tutrial 4 Parameters Tutrial 4: Parameter ptimizatin The aim f this tutrial is t prvide yu with a feeling f hw a few f the parameters that can be set n a QQQ instrument affect SRM results.
More informationPurchase Order Workflow Processing
P a g e 1 Purchase Order Wrkflw Prcessing P a g e 2 Table f Cntents PO Wrkflw Prcessing...3 Create a Purchase Order...3 Submit a Purchase Order...4 Review/Apprve the PO...4 Prcess the PO...6 P a g e 3
More informationCHM112 Lab Graphing with Excel Grading Rubric
Name CHM112 Lab Graphing with Excel Grading Rubric Criteria Pints pssible Pints earned Graphs crrectly pltted and adhere t all guidelines (including descriptive title, prperly frmatted axes, trendline
More informationExperiment #3. Graphing with Excel
Experiment #3. Graphing with Excel Study the "Graphing with Excel" instructins that have been prvided. Additinal help with learning t use Excel can be fund n several web sites, including http://www.ncsu.edu/labwrite/res/gt/gt-
More informationLDS emarket. Section 11 - Catalog Load Process
LDS emarket Sectin 11 - Catalg Lad Prcess Catalg Lad Prcess There are three types f catalgs in LDS emarket: Supplier Direct Web Site An nline catalg f items hsted by the supplier using HTML cding PRG A
More informationTP1 - Introduction to ArcGIS
TP1 - Intrductin t ArcGIS During this practical, we will use ArcGIS (ArcMap and ArcCatalg) t create maps f predictrs that culd explain the bserved bird richness in Switzerland. ArcMap is principally used
More informationCS 477/677 Analysis of Algorithms Fall 2007 Dr. George Bebis Course Project Due Date: 11/29/2007
CS 477/677 Analysis f Algrithms Fall 2007 Dr. Gerge Bebis Curse Prject Due Date: 11/29/2007 Part1: Cmparisn f Srting Algrithms (70% f the prject grade) The bjective f the first part f the assignment is
More informationCHAPTER 24: INFERENCE IN REGRESSION. Chapter 24: Make inferences about the population from which the sample data came.
MATH 1342 Ch. 24 April 25 and 27, 2013 Page 1 f 5 CHAPTER 24: INFERENCE IN REGRESSION Chapters 4 and 5: Relatinships between tw quantitative variables. Be able t Make a graph (scatterplt) Summarize the
More informationHypothesis Tests for One Population Mean
Hypthesis Tests fr One Ppulatin Mean Chapter 9 Ala Abdelbaki Objective Objective: T estimate the value f ne ppulatin mean Inferential statistics using statistics in rder t estimate parameters We will be
More informationWebStats User s Guide (Windows Version) Advanced Internet Technologies, Inc. December 18, 2005
Page 1 f 50 WebStats User s Guide (Windws Versin) WebStats User s Guide (Windws Versin) Advanced Internet Technlgies, Inc. December 18, 2005 Search All Yur Favrite Engines frm a Single Surce with tybit!!!
More informationPurpose: Use this reference guide to effectively communicate the new process customers will use for creating a TWC ID. Mobile Manager Call History
Purpse: Use this reference guide t effectively cmmunicate the new prcess custmers will use fr creating a TWC ID. Overview Beginning n January 28, 2014 (Refer t yur Knwledge Management System fr specific
More informationSkyline Custom Reports and Results Grid
Skyline Custm Reprts and Results Grid The Skyline Targeted Prtemics Envirnment prvides infrmative visual displays f the raw mass spectrmeter data yu imprt int yur Skyline dcuments. It allws yu t wrk with
More informationTRAINING GUIDE. Overview of Lucity Spatial
TRAINING GUIDE Overview f Lucity Spatial Overview f Lucity Spatial In this sessin, we ll cver the key cmpnents f Lucity Spatial. Table f Cntents Lucity Spatial... 2 Requirements... 2 Supprted Mdules...
More informationDEFENSE OCCUPATIONAL AND ENVIRONMENTAL HEALTH READINESS SYSTEM (DOEHRS) ENVIRONMENTAL HEALTH SAMPLING ELECTRONIC DATA DELIVERABLE (EDD) GUIDE
DEFENSE OCCUPATIOL AND ENVIRONMENTAL HEALTH READINESS SYSTEM (DOEHRS) ENVIRONMENTAL HEALTH SAMPLING ELECTRONIC DATA DELIVERABLE (EDD) GUIDE 20 JUNE 2017 V1.0 i TABLE OF CONTENTS 1 INTRODUCTION... 1 2 CONCEPT
More informationCEE3430 Engineering Hydrology HEC HMS Bare Essentials Tutorial and Example
CEE3430 Engineering Hydrlgy HEC HMS Bare Essentials Tutrial and Example Margaret Matter and David Tarbtn February 2010 This tutrial prvides sme bare essentials step by step guidance n starting t use HEC
More informationAP Statistics Notes Unit Two: The Normal Distributions
AP Statistics Ntes Unit Tw: The Nrmal Distributins Syllabus Objectives: 1.5 The student will summarize distributins f data measuring the psitin using quartiles, percentiles, and standardized scres (z-scres).
More informationENSC Discrete Time Systems. Project Outline. Semester
ENSC 49 - iscrete Time Systems Prject Outline Semester 006-1. Objectives The gal f the prject is t design a channel fading simulatr. Upn successful cmpletin f the prject, yu will reinfrce yur understanding
More informationPhysics 2010 Motion with Constant Acceleration Experiment 1
. Physics 00 Mtin with Cnstant Acceleratin Experiment In this lab, we will study the mtin f a glider as it accelerates dwnhill n a tilted air track. The glider is supprted ver the air track by a cushin
More informationSUPPLEMENTARY MATERIAL GaGa: a simple and flexible hierarchical model for microarray data analysis
SUPPLEMENTARY MATERIAL GaGa: a simple and flexible hierarchical mdel fr micrarray data analysis David Rssell Department f Bistatistics M.D. Andersn Cancer Center, Hustn, TX 77030, USA rsselldavid@gmail.cm
More informationRelativity Integration Points Guide. July 3, 2018 Version
Relativity Integratin Pints Guide July 3, 2018 Versin 9.6.50.31 Fr the mst recent versin f this dcument, visit ur dcumentatin website. Table f Cntents 1 Relativity Integratin Pints 4 1.1 Integratin Pints
More informationPSU GISPOPSCI June 2011 Ordinary Least Squares & Spatial Linear Regression in GeoDa
There are tw parts t this lab. The first is intended t demnstrate hw t request and interpret the spatial diagnstics f a standard OLS regressin mdel using GeDa. The diagnstics prvide infrmatin abut the
More informationLab 1 The Scientific Method
INTRODUCTION The fllwing labratry exercise is designed t give yu, the student, an pprtunity t explre unknwn systems, r universes, and hypthesize pssible rules which may gvern the behavir within them. Scientific
More informationCLASS. Fractions and Angles. Teacher Report. No. of test takers: 25. School Name: EI School. City: Ahmedabad CLASS 6 B 8709
SEPTEMBER 07 Math Fractins and Angles CLASS 6 Teacher Reprt Test Taken 4 5 6 7 8 Schl Name: EI Schl City: Ahmedabad CLASS SECTION EXAM CODE 6 B 8709 N. f test takers: 5 6.5 Average.5 9.0 Range (Scres are
More information, which yields. where z1. and z2
The Gaussian r Nrmal PDF, Page 1 The Gaussian r Nrmal Prbability Density Functin Authr: Jhn M Cimbala, Penn State University Latest revisin: 11 September 13 The Gaussian r Nrmal Prbability Density Functin
More informationN C R S I L V E R Q U A N T U M F A Q
N C R S I L V E R Q U A N T U M F A Q V 2 Cntents NCR Silver Quantum Overview... 2 What is NCR Silver Quantum?... 2 Hw is it different than Silver n ios r the Silver Andrid?... 2 Pwer Related Questins...
More informationPipetting 101 Developed by BSU CityLab
Discver the Micrbes Within: The Wlbachia Prject Pipetting 101 Develped by BSU CityLab Clr Cmparisns Pipetting Exercise #1 STUDENT OBJECTIVES Students will be able t: Chse the crrect size micrpipette fr
More informationI. Analytical Potential and Field of a Uniform Rod. V E d. The definition of electric potential difference is
Length L>>a,b,c Phys 232 Lab 4 Ch 17 Electric Ptential Difference Materials: whitebards & pens, cmputers with VPythn, pwer supply & cables, multimeter, crkbard, thumbtacks, individual prbes and jined prbes,
More informationREADING STATECHART DIAGRAMS
READING STATECHART DIAGRAMS Figure 4.48 A Statechart diagram with events The diagram in Figure 4.48 shws all states that the bject plane can be in during the curse f its life. Furthermre, it shws the pssible
More informationI. SEARCH PARAMETERS AND ACCEPTANCE CRITERIA
Revised Publicatin Guidelines fr Dcumenting the Identificatin and Quantificatin f Peptides, Prteins, and Pst Translatinal Mdificatins by Mass Spectrmetry The identificatin f prteins r peptides is cmmnly
More informationSamples. Lutum+Tappert DV-Beratung GmbH
Samples Lutum+Tappert DV-Beratung GmbH EasyMap Cmments abut prvided sample maps Please pen ne f the prvided sample maps by pinting n SAMPLES n the HELP menu (?) after starting EasyMap. Then, select ne
More informationmaking triangle (ie same reference angle) ). This is a standard form that will allow us all to have the X= y=
Intrductin t Vectrs I 21 Intrductin t Vectrs I 22 I. Determine the hrizntal and vertical cmpnents f the resultant vectr by cunting n the grid. X= y= J. Draw a mangle with hrizntal and vertical cmpnents
More informationECE 545 Project Deliverables
ECE 545 Prject Deliverables Tp-level flder: _ Secnd-level flders: 1_assumptins 2_blck_diagrams 3_interface 4_ASM_charts 5_surce_cde 6_verificatin 7_timing_analysis 8_results
More informationEvaluating enterprise support: state of the art and future challenges. Dirk Czarnitzki KU Leuven, Belgium, and ZEW Mannheim, Germany
Evaluating enterprise supprt: state f the art and future challenges Dirk Czarnitzki KU Leuven, Belgium, and ZEW Mannheim, Germany Intrductin During the last decade, mircecnmetric ecnmetric cunterfactual
More informationHow do scientists measure trees? What is DBH?
Hw d scientists measure trees? What is DBH? Purpse Students develp an understanding f tree size and hw scientists measure trees. Students bserve and measure tree ckies and explre the relatinship between
More informationWeb-based GIS Systems for Radionuclides Monitoring. Dr. Todd Pierce Locus Technologies
Web-based GIS Systems fr Radinuclides Mnitring Dr. Tdd Pierce Lcus Technlgies Lcus Technlgies 2014 Overview What is the prblem? Nuclear pwer plant peratrs need t mnitr radinuclides t safeguard the envirnment
More informationPattern Recognition 2014 Support Vector Machines
Pattern Recgnitin 2014 Supprt Vectr Machines Ad Feelders Universiteit Utrecht Ad Feelders ( Universiteit Utrecht ) Pattern Recgnitin 1 / 55 Overview 1 Separable Case 2 Kernel Functins 3 Allwing Errrs (Sft
More informationA water level indicator or other measuring device to determine the current depth to the water.
Fr Aqua4Plus 1.9.7 and later r Aqua4Plus Lite 2.1.1 r later. (Fr earlier versins r if using a PT2X with firmware lwer than 1.5, see Applicatin Nte 9C0152) Intrductin Purpse f this dcument is t prvide a
More informationActivity Guide Loops and Random Numbers
Unit 3 Lessn 7 Name(s) Perid Date Activity Guide Lps and Randm Numbers CS Cntent Lps are a relatively straightfrward idea in prgramming - yu want a certain chunk f cde t run repeatedly - but it takes a
More informationSAP Note Missing documentation on enhancement MDR10001
SAP Nte 303613 - Missing dcumentatin n enhancement Nte Language: English Versin: 2 Validity: Valid Since 31.07.2000 Summary Symptm Missing dcumentatin n SAP enhancement Additinal key wrds CMOD, rder quantity
More informationPhysics 2B Chapter 23 Notes - Faraday s Law & Inductors Spring 2018
Michael Faraday lived in the Lndn area frm 1791 t 1867. He was 29 years ld when Hand Oersted, in 1820, accidentally discvered that electric current creates magnetic field. Thrugh empirical bservatin and
More informationSPH3U1 Lesson 06 Kinematics
PROJECTILE MOTION LEARNING GOALS Students will: Describe the mtin f an bject thrwn at arbitrary angles thrugh the air. Describe the hrizntal and vertical mtins f a prjectile. Slve prjectile mtin prblems.
More informationDifferentiation Applications 1: Related Rates
Differentiatin Applicatins 1: Related Rates 151 Differentiatin Applicatins 1: Related Rates Mdel 1: Sliding Ladder 10 ladder y 10 ladder 10 ladder A 10 ft ladder is leaning against a wall when the bttm
More informationDry-Contact switch Installation Guide
Dry-Cntact switch Installatin Guide Overview The SlarEdge Smart Energy Management slutins allw increasing the self-cnsumptin f a site. One methd used fr this purpse is cntrlling the usage (cnsumptin) f
More informationUnit Project Descriptio
Unit Prject Descriptin: Using Newtn s Laws f Mtin and the scientific methd, create a catapult r trebuchet that will sht a marshmallw at least eight feet. After building and testing yur machine at hme,
More informationAC Switch with Meter Installation Guide Overview
AC Switch with Meter Installatin Guide AC Switch with Meter Installatin Guide Overview The SlarEdge Smart Energy Management slutins allw increasing the self-cnsumptin f a site. One methd used fr this purpse
More informationALE 21. Gibbs Free Energy. At what temperature does the spontaneity of a reaction change?
Name Chem 163 Sectin: Team Number: ALE 21. Gibbs Free Energy (Reference: 20.3 Silberberg 5 th editin) At what temperature des the spntaneity f a reactin change? The Mdel: The Definitin f Free Energy S
More informationPlease Stop Laughing at Me and Pay it Forward Final Writing Assignment
Kirk Please Stp Laughing at Me and Pay it Frward Final Writing Assignment Our fcus fr the past few mnths has been n bullying and hw we treat ther peple. We ve played sme games, read sme articles, read
More informationChapter 3: Cluster Analysis
Chapter 3: Cluster Analysis } 3.1 Basic Cncepts f Clustering 3.1.1 Cluster Analysis 3.1. Clustering Categries } 3. Partitining Methds 3..1 The principle 3.. K-Means Methd 3..3 K-Medids Methd 3..4 CLARA
More informationMisc. ArcMap Stuff Andrew Phay
Misc. ArcMap Stuff Andrew Phay aphay@whatcmcd.rg Prjectins Used t shw a spherical surface n a flat surface Distrtin Shape Distance True Directin Area Different Classes Thse that minimize distrtin in shape
More informationCells though to send feedback signals from the medulla back to the lamina o L: Lamina Monopolar cells
Classificatin Rules (and Exceptins) Name: Cell type fllwed by either a clumn ID (determined by the visual lcatin f the cell) r a numeric identifier t separate ut different examples f a given cell type
More informationWriting Guidelines. (Updated: November 25, 2009) Forwards
Writing Guidelines (Updated: Nvember 25, 2009) Frwards I have fund in my review f the manuscripts frm ur students and research assciates, as well as thse submitted t varius jurnals by thers that the majr
More informationGENESIS Structural Optimization for ANSYS Mechanical
P3 STRUCTURAL OPTIMIZATION (Vl. II) GENESIS Structural Optimizatin fr ANSYS Mechanical An Integrated Extensin that adds Structural Optimizatin t ANSYS Envirnment New Features and Enhancements Release 2017.03
More informationBASD HIGH SCHOOL FORMAL LAB REPORT
BASD HIGH SCHOOL FORMAL LAB REPORT *WARNING: After an explanatin f what t include in each sectin, there is an example f hw the sectin might lk using a sample experiment Keep in mind, the sample lab used
More informationThis section is primarily focused on tools to aid us in finding roots/zeros/ -intercepts of polynomials. Essentially, our focus turns to solving.
Sectin 3.2: Many f yu WILL need t watch the crrespnding vides fr this sectin n MyOpenMath! This sectin is primarily fcused n tls t aid us in finding rts/zers/ -intercepts f plynmials. Essentially, ur fcus
More informationDetermining the Accuracy of Modal Parameter Estimation Methods
Determining the Accuracy f Mdal Parameter Estimatin Methds by Michael Lee Ph.D., P.E. & Mar Richardsn Ph.D. Structural Measurement Systems Milpitas, CA Abstract The mst cmmn type f mdal testing system
More informationThe steps of the engineering design process are to:
The engineering design prcess is a series f steps that engineers fllw t cme up with a slutin t a prblem. Many times the slutin invlves designing a prduct (like a machine r cmputer cde) that meets certain
More informationDepartment of Electrical Engineering, University of Waterloo. Introduction
Sectin 4: Sequential Circuits Majr Tpics Types f sequential circuits Flip-flps Analysis f clcked sequential circuits Mre and Mealy machines Design f clcked sequential circuits State transitin design methd
More informationStandard Title: Frequency Response and Frequency Bias Setting. Andrew Dressel Holly Hawkins Maureen Long Scott Miller
Template fr Quality Review f NERC Reliability Standard BAL-003-1 Frequency Respnse and Frequency Bias Setting Basic Infrmatin: Prject number: 2007-12 Standard number: BAL-003-1 Prject title: Frequency
More informationGuide to Using the Rubric to Score the Klf4 PREBUILD Model for Science Olympiad National Competitions
Guide t Using the Rubric t Scre the Klf4 PREBUILD Mdel fr Science Olympiad 2010-2011 Natinal Cmpetitins These instructins are t help the event supervisr and scring judges use the rubric develped by the
More information2004 AP CHEMISTRY FREE-RESPONSE QUESTIONS
2004 AP CHEMISTRY FREE-RESPONSE QUESTIONS 6. An electrchemical cell is cnstructed with an pen switch, as shwn in the diagram abve. A strip f Sn and a strip f an unknwn metal, X, are used as electrdes.
More informationTemperature sensor / Dual Temp+Humidity
www.akcp.cm Temperature sensr / Dual Temp+Humidity Intrductin Temperature sensrs are imprtant where ptimum temperature cntrl is paramunt. If there is an air cnditining malfunctin r abnrmal weather cnditins,
More informationCHE 105 EXAMINATION III November 11, 2010
CHE 105 EXAMINATION III Nvember 11, 2010 University f Kentucky Department f Chemistry READ THESE DIRECTIONS CAREFULLY BEFORE STARTING THE EXAMINATION! It is extremely imprtant that yu fill in the answer
More informationBasics. Primary School learning about place value is often forgotten and can be reinforced at home.
Basics When pupils cme t secndary schl they start a lt f different subjects and have a lt f new interests but it is still imprtant that they practise their basic number wrk which may nt be reinfrced as
More informationComputational modeling techniques
Cmputatinal mdeling techniques Lecture 4: Mdel checing fr ODE mdels In Petre Department f IT, Åb Aademi http://www.users.ab.fi/ipetre/cmpmd/ Cntent Stichimetric matrix Calculating the mass cnservatin relatins
More informationCESAR Science Case The differential rotation of the Sun and its Chromosphere. Introduction. Material that is necessary during the laboratory
Teacher s guide CESAR Science Case The differential rtatin f the Sun and its Chrmsphere Material that is necessary during the labratry CESAR Astrnmical wrd list CESAR Bklet CESAR Frmula sheet CESAR Student
More informationMATCHING TECHNIQUES. Technical Track Session VI. Emanuela Galasso. The World Bank
MATCHING TECHNIQUES Technical Track Sessin VI Emanuela Galass The Wrld Bank These slides were develped by Christel Vermeersch and mdified by Emanuela Galass fr the purpse f this wrkshp When can we use
More informationGroup Analysis: Hands-On
Grup Analysis: Hands-On Gang Chen SSCC/NIMH/NIH/HHS 3/19/16 1 Make sure yu have the files!! Under directry grup_analysis_hands_n/! Slides: GrupAna_HO.pdf! Data: AFNI_data6/GrupAna_cases/! In case yu dn
More informationLecture 24: Flory-Huggins Theory
Lecture 24: 12.07.05 Flry-Huggins Thery Tday: LAST TIME...2 Lattice Mdels f Slutins...2 ENTROPY OF MIXING IN THE FLORY-HUGGINS MODEL...3 CONFIGURATIONS OF A SINGLE CHAIN...3 COUNTING CONFIGURATIONS FOR
More informationBIOLOGY 101. CHAPTER 17: Gene Expression: From Gene to Protein. The Flow of Genetic Information
BIOLOGY 101 CHAPTER 17: Gene Expressin: Frm Gene t Prtein Gene Expressin: Frm Gene t Prtein: CONCEPTS: 17.1 Genes specify prteins via transcriptin and translatin 17.2 Transcriptin is the DNA-directed synthesis
More informationA B C. 2. Some genes are not regulated by gene switches. These genes are expressed constantly. What kinds of genes would be expressed constantly?
STO-143 Gene Switches Intrductin Bacteria need t be very efficient and nly prduce specific prteins when they are needed. Making prteins that are nt needed fr everyday cell metablism wastes energy and raw
More informationCHAPTER 3 INEQUALITIES. Copyright -The Institute of Chartered Accountants of India
CHAPTER 3 INEQUALITIES Cpyright -The Institute f Chartered Accuntants f India INEQUALITIES LEARNING OBJECTIVES One f the widely used decisin making prblems, nwadays, is t decide n the ptimal mix f scarce
More informationUser Guide: Operation of ActiveAhead Mobile Application
1 (11) User Guide: Operatin f ActiveAhead Mbile Applicatin The ActiveAhead mbile applicatin allws yu t adjust the luminaire parameters f an ActiveAhead slutin. T use this applicatin yu must have an apprved
More informationELT COMMUNICATION THEORY
ELT 41307 COMMUNICATION THEORY Matlab Exercise #2 Randm variables and randm prcesses 1 RANDOM VARIABLES 1.1 ROLLING A FAIR 6 FACED DICE (DISCRETE VALIABLE) Generate randm samples fr rlling a fair 6 faced
More informationHubble s Law PHYS 1301
1 PHYS 1301 Hubble s Law Why: The lab will verify Hubble s law fr the expansin f the universe which is ne f the imprtant cnsequences f general relativity. What: Frm measurements f the angular size and
More informationSubject description processes
Subject representatin 6.1.2. Subject descriptin prcesses Overview Fur majr prcesses r areas f practice fr representing subjects are classificatin, subject catalging, indexing, and abstracting. The prcesses
More informationABSORPTION OF GAMMA RAYS
6 Sep 11 Gamma.1 ABSORPTIO OF GAMMA RAYS Gamma rays is the name given t high energy electrmagnetic radiatin riginating frm nuclear energy level transitins. (Typical wavelength, frequency, and energy ranges
More informationBiplots in Practice MICHAEL GREENACRE. Professor of Statistics at the Pompeu Fabra University. Chapter 13 Offprint
Biplts in Practice MICHAEL GREENACRE Prfessr f Statistics at the Pmpeu Fabra University Chapter 13 Offprint CASE STUDY BIOMEDICINE Cmparing Cancer Types Accrding t Gene Epressin Arrays First published:
More informationSection 6-2: Simplex Method: Maximization with Problem Constraints of the Form ~
Sectin 6-2: Simplex Methd: Maximizatin with Prblem Cnstraints f the Frm ~ Nte: This methd was develped by Gerge B. Dantzig in 1947 while n assignment t the U.S. Department f the Air Frce. Definitin: Standard
More informationLecture 17: Free Energy of Multi-phase Solutions at Equilibrium
Lecture 17: 11.07.05 Free Energy f Multi-phase Slutins at Equilibrium Tday: LAST TIME...2 FREE ENERGY DIAGRAMS OF MULTI-PHASE SOLUTIONS 1...3 The cmmn tangent cnstructin and the lever rule...3 Practical
More informationFinding the Earth s magnetic field
Labratry #6 Name: Phys 1402 - Dr. Cristian Bahrim Finding the Earth s magnetic field The thery accepted tday fr the rigin f the Earth s magnetic field is based n the mtin f the plasma (a miture f electrns
More informationEffective Scientific Writing. Brian Quinn, PhD
Effective Scientific Writing Brian Quinn, PhD brian.quinn@gmit.ie My Backgrund EPA funded envirnmental txiclgist & PI Published 17 papers (inc. invited review) & 2 bk chapters N expert in writing Review
More informationNUROP CONGRESS PAPER CHINESE PINYIN TO CHINESE CHARACTER CONVERSION
NUROP Chinese Pinyin T Chinese Character Cnversin NUROP CONGRESS PAPER CHINESE PINYIN TO CHINESE CHARACTER CONVERSION CHIA LI SHI 1 AND LUA KIM TENG 2 Schl f Cmputing, Natinal University f Singapre 3 Science
More informationCHAPTER 4 DIAGNOSTICS FOR INFLUENTIAL OBSERVATIONS
CHAPTER 4 DIAGNOSTICS FOR INFLUENTIAL OBSERVATIONS 1 Influential bservatins are bservatins whse presence in the data can have a distrting effect n the parameter estimates and pssibly the entire analysis,
More informationAPPLICATION GUIDE (v4.1)
2.2.3 VitalSensrs VS-300 Sensr Management Statin Remte/Relay Guide Implementing Remte-IN/Relay-OUT Digital I/O Fieldbus Objective: Equipment: Becme familiar with the instrument wiring requirements fr the
More informationEditorial Calendar User Guide
Editrial Calendar User Guide Table f Cntents Intrductin... 1 Permissins... 1 Navigatin & Views... 1 Navigatin Menu... 2 Mini Calendar... 2 Calendars in View... 3 Cntent Filtering... 4 Mnthly Calendar...
More informationPart 3 Introduction to statistical classification techniques
Part 3 Intrductin t statistical classificatin techniques Machine Learning, Part 3, March 07 Fabi Rli Preamble ØIn Part we have seen that if we knw: Psterir prbabilities P(ω i / ) Or the equivalent terms
More informationSynchronous Motor V-Curves
Synchrnus Mtr V-Curves 1 Synchrnus Mtr V-Curves Intrductin Synchrnus mtrs are used in applicatins such as textile mills where cnstant speed peratin is critical. Mst small synchrnus mtrs cntain squirrel
More informationInternship Programme of German Business for the Countries of Western Balkans. How to complete your application?
Befre applying please make sure that yu fulfil the precnditins: Undergraduate students wh are enrlled in the 5th semester r higher when applying, Master r PhD students and yung graduates wh graduated after
More informationThermodynamics Partial Outline of Topics
Thermdynamics Partial Outline f Tpics I. The secnd law f thermdynamics addresses the issue f spntaneity and invlves a functin called entrpy (S): If a prcess is spntaneus, then Suniverse > 0 (2 nd Law!)
More informationMATCHING TECHNIQUES Technical Track Session VI Céline Ferré The World Bank
MATCHING TECHNIQUES Technical Track Sessin VI Céline Ferré The Wrld Bank When can we use matching? What if the assignment t the treatment is nt dne randmly r based n an eligibility index, but n the basis
More informationSpace Shuttle Ascent Mass vs. Time
Space Shuttle Ascent Mass vs. Time Backgrund This prblem is part f a series that applies algebraic principles in NASA s human spaceflight. The Space Shuttle Missin Cntrl Center (MCC) and the Internatinal
More informationCreating a pharmacophore from a single protein-ligand complex
1 Creating a pharmacphre frm a single prtein-ligand cmplex basic minutes User Cntrls Advanced cntrls (pt.) Macrmlecule Active site Dwnlad PDB file using -letter cde Discver the crrect ligand Fcus n active
More informationLesson Plan. Recode: They will do a graphic organizer to sequence the steps of scientific method.
Lessn Plan Reach: Ask the students if they ever ppped a bag f micrwave ppcrn and nticed hw many kernels were unppped at the bttm f the bag which made yu wnder if ther brands pp better than the ne yu are
More informationFive Whys How To Do It Better
Five Whys Definitin. As explained in the previus article, we define rt cause as simply the uncvering f hw the current prblem came int being. Fr a simple causal chain, it is the entire chain. Fr a cmplex
More informationTree Structured Classifier
Tree Structured Classifier Reference: Classificatin and Regressin Trees by L. Breiman, J. H. Friedman, R. A. Olshen, and C. J. Stne, Chapman & Hall, 98. A Medical Eample (CART): Predict high risk patients
More information1. Transformer A transformer is used to obtain the approximate output voltage of the power supply. The output of the transformer is still AC.
PHYSIS 536 Experiment 4: D Pwer Supply I. Intrductin The prcess f changing A t D is investigated in this experiment. An integrated circuit regulatr makes it easy t cnstruct a high-perfrmance vltage surce
More informationhttps://goo.gl/eaqvfo SUMMER REV: Half-Life DUE DATE: JULY 2 nd
NAME: DUE DATE: JULY 2 nd AP Chemistry SUMMER REV: Half-Life Why? Every radiistpe has a characteristic rate f decay measured by its half-life. Half-lives can be as shrt as a fractin f a secnd r as lng
More informationNUMBERS, MATHEMATICS AND EQUATIONS
AUSTRALIAN CURRICULUM PHYSICS GETTING STARTED WITH PHYSICS NUMBERS, MATHEMATICS AND EQUATIONS An integral part t the understanding f ur physical wrld is the use f mathematical mdels which can be used t
More informationSection 5.8 Notes Page Exponential Growth and Decay Models; Newton s Law
Sectin 5.8 Ntes Page 1 5.8 Expnential Grwth and Decay Mdels; Newtn s Law There are many applicatins t expnential functins that we will fcus n in this sectin. First let s lk at the expnential mdel. Expnential
More information