course intro

what the course is about

details on topic coverage

learning objectives:

learn to do computations
- efficiently: possibly handling very large data sets
- automatically: using scripts to repeat tasks (and avoid manual errors)
- reproducibly: by oneself or by others
- collaboratively: sharing work with a version control system
demonstrate ability to adapt to change

what the course is not about:

learn how to run specific software / bioinformatics pipelines (use google, online manuals & resources)
learn how to use R (other courses)
learn statistical concepts / techniques (other courses)

why should we learn these things?

demands from the modern professional world: research & industry
cautionary tale: “Duke Saga”. Research with multiple serious errors, reviewed by statisticians Baggerly and Coombes. Results could not be reproduced, insufficient information to reproduce all the steps. “forensic bioinformatics”. read their paper and watch the youtube video (13 minutes) for the story.
- “common errors are simple, and simple errors are common”
- poor documentation can lead to errors and irreproducibility. document:
  - data
  - methods, software versions
  - code
talk on reproducible research by Karl Broman. pdf with notes here. Slide #14 is so true: Your closest collaborator is you six months ago, but you don’t reply to emails.”

expectations

bring your laptop ~~to class~~ every time
very active participation. no practice = no learning.
- try things out, spend time debugging, again and again
- ask questions (on Piazza, office hours etc.)
- help others with their practical roadblocks (in Piazza etc.)
your learning objectives? expectations? fill out start-of-semester survey on Canvas.

assignments and grading

read the syllabus on Canvas.

logistics

Your laptop is going to be your minion and best friend. Invest in it!

Hardware requirement: Linux or Mac.

need to use the shell, bash or zsh (this tool won’t change!)
need admin access: to have the freedom to install new software or tweak which compiler or Python version (etc.) you system uses.
pick an old laptop in your parents’ or friends’ basement, presumably old and slow. Wipe its OS and install some LTS (long term support) release of Ubuntu. Version 20.04.1 recommends
- 2 GHz dual core processor
- 4 GB system memory
- 25 GB of free hard drive space
- Either a DVD drive or a USB port for the installer media
- Internet access is helpful
but choose a light-weight environment (how the desktop looks like and what tools are preinstalled) for lower requirements (avoid Unity and Gnome).

motivating example: data manipulation

Data manipulation & data cleaning from one of my student’s research: extract various pieces of information from various files such as this “out” file TestResults/out files/net1_snaq.out:

(ECH3937,((Dic586,DzeEch1591):0.39334426457355115,((((BspEniD312,BsaATCC15712):0.313091357476667,((PcaPC1,(PcaPCC21,WPP1692):1.1457045168568845):0.08725049544490777,(SCRI1043,((PectoSCC3193,Pwa43316):0.858533139429174,#H20:1.2894166676352883::0.022562841930608746):0.09559815984571758):0.4382834061748707):2.5022258780461746):1.4087025649051665,(((GCDA,GBAG):2.2215234026418282,((Pae1,PstDC3000):3.5532626847828177,(VFI114,VchN16961):2.514723407664476):1.3114662776537342):0.41902892411289594)#H20:1.1087410295507665::0.9774371580693912):1.7110632803748822,Dpa2511):1.506271879442207):0.7569747895374156,Ddi453); -Ploglik = 3440.8180547004067
 Dendroscope: (ECH3937,((Dic586,DzeEch1591):0.39334426457355115,((((BspEniD312,BsaATCC15712):0.313091357476667,((PcaPC1,(PcaPCC21,WPP1692):1.1457045168568845):0.08725049544490777,(SCRI1043,((PectoSCC3193,Pwa43316):0.858533139429174,#H20:1.2894166676352883):0.09559815984571758):0.4382834061748707):2.5022258780461746):1.4087025649051665,(((GCDA,GBAG):2.2215234026418282,((Pae1,PstDC3000):3.5532626847828177,(VFI114,VchN16961):2.514723407664476):1.3114662776537342):0.41902892411289594)#H20:1.1087410295507665):1.7110632803748822,Dpa2511):1.506271879442207):0.7569747895374156,Ddi453);
 Elapsed time: 11648.984309726 seconds in 10 successful runs
-------
List of estimated networks for all runs:
 (ECH3937,((Dic586,DzeEch1591):0.39334426457355115,((((BspEniD312,BsaATCC15712):0.313091357476667,((PcaPC1,(PcaPCC21,WPP1692):1.1457045168568845):0.08725049544490777,(SCRI1043,((PectoSCC3193,Pwa43316):0.858533139429174,#H20:1.2894166676352883::0.022562841930608746):0.09559815984571758):0.4382834061748707):2.5022258780461746):1.4087025649051665,(((GCDA,GBAG):2.2215234026418282,((Pae1,PstDC3000):3.5532626847828177,(VFI114,VchN16961):2.514723407664476):1.3114662776537342):0.41902892411289594)#H20:1.1087410295507665::0.9774371580693912):1.7110632803748822,Dpa2511):1.506271879442207):0.7569747895374156,Ddi453);, with -loglik 3440.8180547004067
 (VFI114,VchN16961,(((GBAG,GCDA):2.5245419478720663,(((((Ddi453,ECH3937):0.6047267342464384,(Dic586,DzeEch1591):0.3403176012248513):1.9059445907036108,Dpa2511):2.235321253925316,(BsaATCC15712,((PcaPCC21,(((WPP1692,PcaPC1):4.840121005469344e-81,SCRI1043):1.5701029169080017e-81,#H20:::0.3236896049860076):1.352198753587325e-17):0.05736002957738657,(Pwa43316,PectoSCC3193):1.5238322108331215):2.51329903340477):1.036277594288562):0.0,(BspEniD312)#H20:::0.6763103950139924):1.7190095175499105):1.530594461241091,(Pae1,PstDC3000):4.995850727915352):2.562424468068505);, with -loglik 19269.16345936403
 ((((PectoSCC3193,Pwa43316):3.553610733771546e-15,SCRI1043):0.6474185172594675,(BsaATCC15712,((BspEniD312,((Dpa2511,((DzeEch1591,Dic586):0.40820601146043234,(ECH3937,Ddi453):0.8757625508985754):1.6724150659934216):2.183643473060728,((GBAG,GCDA):3.1451583907332092,((Pae1,PstDC3000):4.509705244575739,(VFI114,VchN16961):2.503235768283856):1.5078417948141687):1.5959002904387598):1.553542222136306):0.0)#H22:1.309389116513644e-15::0.9127687744114756):10.0):0.04995813473096922,(#H22:9.048390395573063e-16::0.08723122558852431,PcaPC1):2.2346481928265355e-18,(PcaPCC21,WPP1692):1.552683790646415);, with -loglik 6890.772908596581
 (VFI114,VchN16961,(((GBAG,GCDA):2.2181192485056758,((Dpa2511,((DzeEch1591,Dic586):0.3916156240560825,(ECH3937,Ddi453):0.7566722278726479):1.5074684429287624):1.747429526882279,((((PectoSCC3193,Pwa43316):0.9501732839655112,SCRI1043):0.4029626050630284,(PcaPCC21,((WPP1692,PcaPC1):0.0)#H20:0.0::0.9722639735503795):0.4027554189070717):2.2721218845628948,(#H20:0.0003038114855103211::0.02773602644962043,(BsaATCC15712,BspEniD312):0.33463588910738173):0.0):1.229804645020795):1.3399682651446452):1.3120033729922145,(Pae1,PstDC3000):3.5600301681303845):2.51818214370805);, with -loglik 5620.196528113887
 (ECH3937,Ddi453,((Dpa2511,((((PcaPC1,(PcaPCC21,WPP1692):1.1429852032707186):0.09620215996092102,(SCRI1043,(Pwa43316,PectoSCC3193):0.9511872865590026):0.42678193109726004):2.1183264683380596,(BspEniD312,BsaATCC15712):0.3384076580894693):1.216974452459672,((GBAG,GCDA):2.194352317062987,(((Pae1,PstDC3000):3.5397209154481932,(VFI114,VchN16961):2.5111214631509617):0.4794476644505572)#H20:0.9467698406332375::0.9884611277426241):1.4240870413695534):1.8521032319317305):1.6037951419775782,(DzeEch1591,(Dic586,#H20:0.05109572126928388::0.011538872257375885):0.4397058985891824):0.3943173907613837):0.7523611860416453);, with -loglik 3793.0442212805383
 (ECH3937,(((((GCDA,GBAG):2.193756843189924,(((VFI114,VchN16961):2.5207381162686846,(Pae1,PstDC3000):3.554378937046041):0.01233174464049745)#H20:1.497720306073061::0.9892992939236428):1.4296038206660144,((BsaATCC15712,BspEniD312):0.3345621679479068,((PcaPC1,(PcaPCC21,WPP1692):1.1449069248382384):0.09309828120666166,(SCRI1043,(Pwa43316,PectoSCC3193):0.9526041635444833):0.42668782398545746):2.118870240664439):1.2167087667210865):1.8440376842575519,Dpa2511):1.5957887532496429,(DzeEch1591,(Dic586,#H20:4.675334247257724::0.010700706076357177):0.0077445203460371655):0.3952345483913463):0.7532993567084834,Ddi453);, with -loglik 3789.1508233434643
 (VFI114,VchN16961,(((GBAG,GCDA):2.212475599100721,(((((DzeEch1591,Dic586):0.3696509747311919,(ECH3937,Ddi453):0.756737928774276):1.5112758720613992,Dpa2511):1.684052571235145,(((((PcaPCC21,WPP1692):1.1469873337860346,PcaPC1):0.09038485166954024,((PectoSCC3193,Pwa43316):0.9555743576515744,SCRI1043):0.4255967306373895):2.113114818846118,(BsaATCC15712,BspEniD312):0.3361897404293803))#H20:2.093864102636834::0.9314636030199334):1.162510627859383,#H20:6.171613091377723e-8::0.06853639698006661):0.36234994766300677):1.310324100987545,(Pae1,PstDC3000):3.6037463809694015):2.5373275910417945);, with -loglik 3821.5271175693492
 ((WPP1692,PcaPCC21):1.0534575224123381,((SCRI1043,(Pwa43316,PectoSCC3193):0.9488036980689983):0.0,#H22:9.992377816436747::0.3235310400449231):0.6620187375621733,(PcaPC1,(((BspEniD312,BsaATCC15712):0.33343475782982623,((Dpa2511,((ECH3937,Ddi453):0.7530463904900576,(DzeEch1591,Dic586):0.38997603702161565):1.5066595347385965):1.7486516843928388,((GCDA,GBAG):2.224283684607174,((VchN16961,VFI114):2.5102867402698825,(Pae1,PstDC3000):3.5487706559153787):1.3130259481090099):1.3407781540044517):1.2265176226740198):1.9732658721762155)#H22:0.2794988181403773::0.6764689599550768):0.22661513908037734);, with -loglik 3770.6791156388645
 (((Dpa2511,(((BspEniD312,BsaATCC15712):0.3346621630454019,((PcaPC1,(WPP1692,PcaPCC21):1.1442123144680205):0.09306634431412385,((Pwa43316,PectoSCC3193):0.9526331443229515,SCRI1043):0.4271180729130922):2.1187983635203205):1.216970952460887,((GBAG,GCDA):2.1954878077368796,(((PstDC3000,Pae1):3.55278287210519,(VchN16961,VFI114):2.5204195787957584):0.0)#H22:1.5048013291163698::0.9897342850994104):1.4267386398600983):1.8421285001624097):1.597605850292273,(Ddi453,ECH3937):0.7532176353973834):0.3967618687594186,DzeEch1591,(Dic586,#H22:0.006261881582570027::0.010265714900589622):0.35723839150575165);, with -loglik 3786.7201402041833
 (VFI114,VchN16961,((Pae1,PstDC3000):3.559990458370163,((GCDA,GBAG):2.218012119547241,(((BsaATCC15712,BspEniD312):0.33455337500466675,(((SCRI1043,(Pwa43316,(PectoSCC3193)#H22:::0.9715644289314767):1.0967310149501057):0.45575302685090346,(PcaPC1,(WPP1692,PcaPCC21):1.1421245266445263):0.08234532616324368):2.210036261995772,#H22:::0.028435571068523364):8.160583229878246e-6):1.2275791123554678,(((ECH3937,Ddi453):0.7567033876290241,(DzeEch1591,Dic586):0.3916330806387961):1.5074252624245137,Dpa2511):1.7474327640290075):1.3399421382797148):1.3119914628188931):2.5181349183423207);, with -loglik 3864.1900537877186
-------

or this other “out” file TestResults/out files/Timetest1_snaq.out:

(ECH3937,Ddi453,((Dic586,DzeEch1591):0.39151452022020755,(Dpa2511,(((BsaATCC15712,BspEniD312):0.31165264651122426,((PcaPC1,(PcaPCC21,WPP1692):1.144025891196133):0.0876790364165445,(((PectoSCC3193,Pwa43316):0.9529701731377197,SCRI1043):0.0632647451890301,#H20:8.251812487790279e-7::0.023694403794416646):0.37365021164620515):2.5071408957817876):1.4168426104118295,(((GCDA,GBAG):2.21912632231476,((Pae1,PstDC3000):3.565361799130726,(VFI114,VchN16961):2.518277890640175):1.3136037135425378):0.42011126229987183)#H20:1.1184877095177088::0.9763055962055833):1.7090991861969702):1.5074073219469928):0.7563231659538783); -Ploglik = 3443.958828187268
 Dendroscope: (ECH3937,Ddi453,((Dic586,DzeEch1591):0.39151452022020755,(Dpa2511,(((BsaATCC15712,BspEniD312):0.31165264651122426,((PcaPC1,(PcaPCC21,WPP1692):1.144025891196133):0.0876790364165445,(((PectoSCC3193,Pwa43316):0.9529701731377197,SCRI1043):0.0632647451890301,#H20:8.251812487790279e-7):0.37365021164620515):2.5071408957817876):1.4168426104118295,(((GCDA,GBAG):2.21912632231476,((Pae1,PstDC3000):3.565361799130726,(VFI114,VchN16961):2.518277890640175):1.3136037135425378):0.42011126229987183)#H20:1.1184877095177088):1.7090991861969702):1.5074073219469928):0.7563231659538783);
 Elapsed time: 16688.01510346 seconds in 10 successful runs
-------
List of estimated networks for all runs:
 (ECH3937,Ddi453,((Dic586,DzeEch1591):0.3916223389169537,(Dpa2511,(((BsaATCC15712,BspEniD312):0.3128260626881626,(PcaPC1,((SCRI1043,((PectoSCC3193,Pwa43316):0.6977437173196366,#H20:0.00022822386439850124::0.021630732814455052):0.26322537066459134):0.4236629591108912,(PcaPCC21,WPP1692):1.1890466239510304):0.06863934472914392):2.4773007202770576):1.4053376341094526,(((GCDA,GBAG):2.219164745964012,((PstDC3000,Pae1):3.5602401877744643,(VFI114,VchN16961):2.5183186557471093):1.3135338210943872):0.41032277572157794)#H20:1.1138891991703652::0.978369267185545):1.7118998331253241):1.5069910040504322):0.7566818252183738);, with -loglik 3455.845945853218
 (VFI114,VchN16961,((((Dpa2511,((ECH3937,(Ddi453)#H20:::0.9940317642071066):0.7909101959471819,(Dic586,DzeEch1591):0.3822022037813626):1.5729758170682475):1.7827505483353387,((BsaATCC15712,BspEniD312):0.3337206942159198,(((PectoSCC3193,Pwa43316):0.9523881593998712,SCRI1043):0.4263694627890546,((PcaPCC21,WPP1692):1.1443644073470125,(PcaPC1,#H20:::0.005968235792893377):1.459335224099927):0.0934172793433709):2.1361816669883664):1.2369595960158875):1.3378100318296535,(GCDA,GBAG):2.2181613686042736):1.3118574211203706,(Pae1,PstDC3000):3.5620157597292295):2.5171717848786104);, with -loglik 3860.533441026289
 (VFI114,VchN16961,(((GCDA,GBAG):2.2180451724547128,((Dpa2511,((ECH3937,Ddi453):0.7470303514949284,(Dic586,(DzeEch1591)#H20:::0.994771261343114):0.4083904741512361):1.5647832090680156):1.7807472197470362,((BsaATCC15712,BspEniD312):0.33353223019842365,((SCRI1043,(PectoSCC3193,(Pwa43316,#H20:::0.005228738656885995):0.10184589942412053):0.9563893187362575):0.4295184565038544,(PcaPC1,(PcaPCC21,WPP1692):1.1447460190010872):0.09241025146502349):2.138754739951621):1.236388839988299):1.3378875879930074):1.3119542771562265,(Pae1,PstDC3000):3.559964423795921):2.5181376787449845);, with -loglik 3859.115780423511
 (VFI114,(((GCDA,GBAG):2.2116293771387436,(((((PectoSCC3193,Pwa43316):0.9451763936198495,SCRI1043):0.4276126604275862,(PcaPC1,(PcaPCC21,WPP1692):1.1442515087738958):0.09257741297938635):2.1175503858573657,(BsaATCC15712,BspEniD312):0.3358694731956836):1.226419818151741,(Dpa2511,((ECH3937,Ddi453):0.7537967494400539,(Dic586,DzeEch1591):0.3918148459412738):1.5051842841458647):1.7498955131059477):1.3418708024902517):1.212458369009057,((PstDC3000,Pae1):3.647142996017561)#H20:0.0::0.9175175496088633):4.44195280505641,(VchN16961,#H20:0.003097631251670284::0.08248245039113664):0.12357098930534696);, with -loglik 3880.752407454445
 (Pwa43316,(SCRI1043,((PcaPC1,(PcaPCC21,WPP1692):1.1334868472726147):0.015529070014493173,(((BsaATCC15712,BspEniD312):0.334192507684605,((Dpa2511,((ECH3937,Ddi453):0.7637187370250744,(Dic586,DzeEch1591):0.39454426004379634):1.5004547626395341):1.7516952494614373,((GCDA,GBAG):2.1979948685600146,((Pae1,PstDC3000):3.565208708518564,(VFI114,VchN16961):2.5451573307659827):1.3136886241612056):1.3414962402868322):1.2303311675499125):0.9886797414707493)#H20:2.4246357026184118::0.9072559440190524):0.5775689462229046):1.2184942668958334,(PectoSCC3193,#H20:0.012726416987990588::0.09274405598094757):0.07370961607455255);, with -loglik 3811.554199979079
 (VFI114,VchN16961,(((GCDA,GBAG):2.213866261637645,(((BsaATCC15712,BspEniD312):0.3357443180077425,(((PectoSCC3193,Pwa43316):0.952020727134612,SCRI1043):0.4261925401517078,(PcaPC1,(PcaPCC21,WPP1692):1.144072670650649):0.0941130880421839):2.119205380854781):1.2182342965189237,(Dpa2511,(((ECH3937,Ddi453):0.7574919898685711,(Dic586,DzeEch1591):0.3908116183920976):0.03198033167351987)#H20:1.763212262416741::0.9924168215315269):1.8874765424136433):1.385918971638839):1.3581769509836341,((Pae1,PstDC3000):0.45961881403585547,#H20:0.0017264888860279942::0.007583178468473104):3.378616184478208):2.5098725180135033);, with -loglik 3777.823939751652
 (ECH3937,Ddi453,((Dic586,DzeEch1591):0.39151452022020755,(Dpa2511,(((BsaATCC15712,BspEniD312):0.31165264651122426,((PcaPC1,(PcaPCC21,WPP1692):1.144025891196133):0.0876790364165445,(((PectoSCC3193,Pwa43316):0.9529701731377197,SCRI1043):0.0632647451890301,#H20:8.251812487790279e-7::0.023694403794416646):0.37365021164620515):2.5071408957817876):1.4168426104118295,(((GCDA,GBAG):2.21912632231476,((Pae1,PstDC3000):3.565361799130726,(VFI114,VchN16961):2.518277890640175):1.3136037135425378):0.42011126229987183)#H20:1.1184877095177088::0.9763055962055833):1.7090991861969702):1.5074073219469928):0.7563231659538783);, with -loglik 3443.958828187268
 (VFI114,VchN16961,(((GCDA,GBAG):2.219460035105914,((Dpa2511,(((ECH3937,Ddi453):0.75630888011499,(Dic586,DzeEch1591):0.3919875100972792):1.380739910125236,#H20:::0.010247944712692417):0.1267063939441514):1.7556400603164963,(((((Pwa43316,(PectoSCC3193)#H20:::0.9897520552873076):1.0203848918799054,SCRI1043):0.4442368954687679,(PcaPC1,(PcaPCC21,WPP1692):1.1431289589640605):0.08882274906772937):2.201511576092636,BspEniD312):0.0,BsaATCC15712):1.2645226824391311):1.3377070859820448):1.3118900769122575,(Pae1,PstDC3000):3.5515426626571953):2.515647137851658);, with -loglik 4357.230840522077
 (VFI114,VchN16961,(((GCDA,GBAG):2.2183132507826904,(((Dpa2511,((ECH3937,Ddi453):0.7567273128941133,(Dic586,DzeEch1591):0.39151150339747):1.5071812690507407):1.721566100927654,((BsaATCC15712,BspEniD312):0.2897689849762642,((((PectoSCC3193,Pwa43316):0.9525864229583921,SCRI1043):0.42692988906485313,(PcaPC1,(PcaPCC21,WPP1692):1.1449532226110368):0.09304539465538224):0.6838826946843389)#H20:2.3273420820899653::0.969250753611784):1.4404006054681064):1.4464278717313024,#H20:1.2813081230801888::0.03074924638821598):0.0):1.3120148804021463,(Pae1,PstDC3000):3.5615515442678705):2.5179082718561263);, with -loglik 3465.6935439833105
 (VFI114,VchN16961,(((GCDA,GBAG):2.218398156745566,((Dpa2511,((ECH3937,Ddi453):0.7565245329816281,((Dic586,DzeEch1591):0.3074760295098175,#H20:::0.01057544767069923):0.08439636130940043):1.5263962399612987):1.7676594274287591,((BsaATCC15712,(BspEniD312)#H20:::0.9894245523293008):0.35068273430616315,(((PectoSCC3193,Pwa43316):0.9522720970942834,SCRI1043):0.42662648477461573,(PcaPC1,(PcaPCC21,WPP1692):1.1446634305897092):0.0930095443582278):2.108996812337079):1.2518446488144161):1.3376850915400154):1.3120369837552903,(Pae1,PstDC3000):3.5616003865640833):2.518746338077192);, with -loglik 3892.1805493222896
-------

Each file was the result of one analysis. Hundreds of analyses were made. Each analysis also had a “log” file, e.g. TestResults/log files/Timetest1_snaq.log starting like this:

optimization of topology, BL and inheritance probabilities using:
 hmax = 1,
 tolerance parameters: ftolRel=1.0e-5, ftolAbs=1.0e-6,
                       xtolAbs=0.0001, xtolRel=0.001.
 max number of failed proposals = 10, multiplier M = 10000.
rootname for files: temtest1_snaq
BEGIN: 10 runs on starting tree (VFI114,VchN16961,(((GCDA,GBAG):2.21807813924953,((Dpa2511,((ECH3937,Ddi453):0.7566916943696904,(Dic586,DzeEch1591):0.39164053319430225):1.5074406866092167):1.747431936458303,((BsaATCC15712,BspEniD312):0.33456697190000023,(((PectoSCC3193,Pwa43316):0.9524725883536365,SCRI1043):0.42667192097520906,(PcaPC1,(PcaPCC21,WPP1692):1.1448942055036169):0.09303348762204595):2.1191171552256183):1.2281031678188656):1.3399415660611986):1.3119963967965944,(Pae1,PstDC3000):3.560015689796989):2.518148088969418);

main seed 30312
seed: 30312 for run 1
Sat Jun 11 16:35:20 2016
...
---------------------
seed: 1440 for run 2
Sat Jun 11 17:47:11 2016
...

Data cleanaing task, before some downstream analysis: extract key information from each file, then combine the data points from each pair of files into a summary table like this:

analysis,hmax,number of runs,Nfails,ftolAbs,ftolRel,xtolAbs,xtolRel,first seed,best seed,number of loglik under 3460,number of loglik under 3450,number of loglik under 3440,-loglik,best run time,total CPU time
net1_snaq,1,10,100,0.000001,0.00001,0.0001,0.001,3322,3322,1,1,0,3440.8181,16000,150000
Best Starting Tree,0,1,100,0.000001,0.00001,0.0001,0.001,66077,66077,0,0,0,3917.9621,10085,10085
Best Model,1,10,100,0.000001,0.00001,0.0001,0.001,36252,14351,4,4,2,3439.7454,12012,88579.31
Timetest1,1,10,10,0.000001,0.00001,0.0001,0.001,30312,81138,2,1,0,3443.9588,1598,16688.02
Timetest2,1,10,25,0.000001,0.00001,0.0001,0.001,28669,28669,4,1,0,3445.5654,2607,37137.96
Timetest6,1,10,25,0.000001,0.00001,0.0001,0.001,14351,14351,4,3,3,3439.8319,4940,39287.8
Timetest3,1,10,100,0.1,0.1,0.0001,0.001,66086,86464,0,0,0,3579.9085,2239,12630.99
Timetest4,1,10,100,0.01,0.01,0.0001,0.001,62366,62366,0,0,0,3471.5565,3526,21942.35
Timetest5,1,10,100,0.005,0.005,0.0001,0.001,3888,25572,2,1,0,3443.9379,3746,23949.38
Timetest7,1,10,100,0.005,0.005,0.0001,0.001,14351,14351,5,5,0,3442.2165,2351,29822.15
Timetest8,1,10,100,0.000001,0.00001,0.001,0.1,15989,68739,3,2,1,3439.8619,2091,51589.34
Timetest9,1,10,50,0.0001,0.00001,0.0001,0.001,45123,97830,1,1,0,3450.3233,1772,34831.47
Timetest10,1,10,50,0.00001,0.0001,0.0001,0.001,37792,44249,0,0,0,3462.3852,3842,29394.46
Timetest11,1,10,50,0.000005,0.00001,0.0001,0.001,25765,78407,2,2,0,3444.0098,12200,67926.5
Timetest12,1,10,50,0.000001,0.00001,0.01,0.1,39416,74437,4,0,0,3452.1753,1790,18935.63
Timetest13,1,10,100,0.00001,0.00001,0.01,0.1,38112,82736,3,1,1,3439.7857,3131,31456.99

We want to write code to perform this task

to make it reproducible
to avoid human errors
because we will likely run more analyses and we will likely want to re-do the task again.

text editor

I highly recommend VS Code, for all platforms. To launch VS Code from the command line via code, Mac users will first need to follow these instructions. VS Code is free, it is excellent to maintain a project with many different files (e.g. to look up the definition of a function located in a different file, or search/replace a variable name in all files within a folder) it is fast (even on huge data files), it has lots of plug-ins, etc. Alternatives:

TextWrangler or Atom for Mac users
gedit, Emacs or Atom for Linux users
nano for a command-line editor, useful when working on a remote computer cluster, for instance.

In the terminal, type which code, or which emacs (or which nano or which edit) to see if you have them installed, emacs --version to see the version.