Beginning Perl for Bioinformatics

babbage writes:"As the banner above the title of James Tisdall's Beginning Perl for Bioinformatics indicates, this book is 'an introduction to Perl for biologists.' What the banner doesn't mention is that it's also an introduction to biology and bioinformatics for Perl programmers, and it's also an introduction to both Perl *and* biology for people that have never really been exposed to either field. The author has clearly thought a lot about making one book to please these different audiences, and he has pulled it off nicely, in a way that manages to explain basic topics to people learning about each field for the first time while not coming off as condescending or slow-paced to those that might already have some exposure to it." Read on for the rest of his review. Beginning Perl for Bioinformatics author James Tisdall pages 400 publisher O'Reilly & Associates rating 8 reviewer babbage ISBN 0-596-00080-4 summary Well-balanced approach to applying Perl's sorting and analytical abilities to the field of bioinformatics.

Superficially, this book isn't all that different from a lot of introductory Perl books: the Perl material starts out with an overview of the language, followed by a crash course on installing Perl, writing programs, and running them. From there, it goes on to introduce all the various language constructs, from variables to statements to subroutines, that any programmer is going to have to get comfortable with. Pretty run of the mill so far. Tisdall starts with two interesting assumptions, though: [1] that the reader may have never written a computer program before, and so needs to learn how to engineer a robust application that will do its job efficiently and well, and [2] that the reader wants to know how to write programs that can solve a series of biological problems, specifically in genetics and proteomics.

As such, there is at least as much material about the problems that a biologist faces and the places she can go to get the data she needs as there is about the issues that a Perl programmer needs to be aware of. The author introduces the reader to the basics of DNA chemistry, the cellular processes that convert DNA to RNA and then proteins, and a little bit about how and why this is important to the biologist and what sorts of information would help a biologist's research. The main sources of public genetic data are noted, and the often confusing -- and huge -- datafiles that can be obtained from these sources are examined in detail.

With the code he presents for solving these problems, Tisdall makes a point of not falling into the indecipherable-Perl trap: this is a useful language, well-suited to the essentially text-analysis problems that bioinformatics means, and he doesn't want to encourage the kind of dense, obscure, idiomatic coding style that has given Perl an undeservedly bad reputation. Some of Perl's more esoteric constructs are useful, and they show up when they're needed, but they're left out when they would only serve to confuse the reader. This is a good decision.

Rather, the focus is on teaching readers how to solve biological problems with a carefully developed library of code that happens to leverage some of Perl's most useful properties. The result is pretty much a biologist's edition of Christiansen & Torkington's Perl Cookbook or Dave Cross' Data Munging With Perl. The author presents a series of issues that a working bioinformaticist might have to deal with daily -- parsing over BLAST, GenBank, and PDB files, finding relevant motifs in that parsed data, and preparing reports about all of it. If a bioinformaticist's job is to be able to report on interesting patterns from these various sources, then following the programming techniques that Tisdall explains in clear, easy-to-follow prose would be an excellent way to go about doing it.

And when I say "programming techniques," note that I'm not specifically mentioning Perl. The code in this book is clear and organized, and all programs are carefully decomposed into logical subroutines that are then packaged up into a library file that each later sample program gets to draw from. Each new program typically contains a main section of a dozen lines of code or less, followed by no more than two or three new subroutines, along with calls to routines written earlier and called from the BeginPerlBioinfo.pm that is built up as the book progresses. Each sample is typically preceded by a description of what it's trying to accomplish and followed by a detaild description of how it was done, as well as suggestions of other ways that might have worked or not worked.

This modular approach is fantastic -- too many Perl books seem to focus so heavily on the mechanics of getting short scripts to work that they lose sight of how to build up a suite of useful methods and, from those methods, to develop ever-more-sophisticated applications. It isn't quite object-oriented programming, but that's clearly where Tisdall is headed with these samples, and given a few more chapters he probably would have started formally wrapping some of this code into OO packages.

If I have a complaint with the book, in fact, it's that Tisdall doesn't go any further: everything is good, but it ends too soon. Seemingly important topics such as OO programming, XML, graphics (charts & GUIs), CGI, and DBI are mentioned only in passing, under "further topics" in the last chapter. I also have a feeling that some of the biology was shorted, and the book barely touches upon the statistical analysis that probably is a critical aspect of the advanced bioinformaticist's toolbox. I can understand wanting to keep the length of a beginner's book relatively short, and this was probably the right decision, but it would have been nice to see some of the earlier sample problems revisited in these new contexts by, for example, formally making an OO library, showing a sample program that provided a web interface to some of the methods already written, or presenting code that presented results as XML or exchanged them with a database.

But these are minor quibbles, and if the reader is comfortable with the material up to this point, she shouldn't have a hard time figuring out how to go a step further and do these things alone. It's a solid book, and one that should be able to get people learning Perl, genetics, or both up to speed and working on real world problems quickly.

You can purchase Beginning Perl for Bioinformatics at Fatbrain. Want to see your own review here? Read the review guidelines first, then use Slashdot's webform.

Comments

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Dmjjmugle gq qmkc gldmpk_rgml _`msr rfc asjr.

/. @_qga Gldmpk_rgml md "Qmsrf Afgl_ Afspaf"

"Qmsrf Afgl_ Afspaf" u_q dmslbcb `w Emle Qfclejg_le* _ dmpkcp icw kck`cp md rfc asjr "Afspaf md ?jj P_lecq" (afs_l d_le ucg hg_m fsg). Emle gq _ k_l md dmprw-lglc wc_pq md _ec _lb dpmk X_mw_le Agrw* Fs`cg Npmtglac. Fgq mrfcp l_kcq _pc Emle B_jg* Emle Qfclejg _lb fgq nqcsbmlwk gq Xgml* `sr fgq dmjjmucpq a_jj fgk "rc_afcp." Gl /77.* Emle Qfclejg_le f_b qmkc bgq_epcckclr ugrf Vs Wmlexc* rfc afgcd jc_bcp md "Afspaf md ?jj P_lecq." Rfsq fc e_rfcpcb qmkc mrfcp icw kck`cpq _lb jcdr Vs Wmlexc _lb qcr sn "Qmsrf Afgl_ Afspaf" gl Xfmle W_le Agrw* Fs`cg Npmtglac. @_qcb ml "Bp_drq md Afspaf @_qga Amlqrpsargml" mpgegl_jjw bp_ul msr dmp "Afspaf md ?jj P_lecq*" Emle Qfclejg_le upmrc "Emb'q Dmpctcp _lb Ctcp" _q rfc bmarpglc dmp "Qmsrf Afgl_ Afspaf." Gl Dc`ps_pw /771* Emle _jqm k_bc "Qmsrf Afgl_ Rfgprccl Psjcq*" rfc esgbgle npglagnjcq dmp "Qmsrf Afgl_ Afspaf" _argtgrgcq* gl ufgaf fc _btma_rcb rm "`pgle rfc emqncj rm rfc ufmjc l_rgml* asjrgt_rc _ Afpgqr-jgic asjrspc* _lb apc_rc _ l_rgml-ugbc afspaf." Fc _jqm apgcb msr rm fgq dmjjmucpq rm "nsr ml rfc ufmjc _pkmp egtcl `w rfc Jmpb* dgefr _ `jmmbw `_rrjc ugrf rfc bctgj (pcdcppgle rm rfc emtcplkclr) rgjj rfc clb* qm rf_r rfc Q_r_l'q (pcdcppgle rm rfc Amkkslgqr N_prw) _srfmpgrw ugjj `c bcqrpmwcb _lb rfc iglebmk md rfc ctcp-j_qrgle Emb ugjj `c cqr_`jgqfcb."

"Qmsrf Afgl_ Afspaf" f_q _ qrpgar mpe_lgx_rgml_j qwqrck md dmsp jctcjq: amslagj* jg_gqml _qqck`jw* xmlc* _lb kccrgle nj_ac (wg fsg* hg_m rmle fsg* ng_l* hs fsg bg_l). Rfc amslagj gq rfc rmn jctcj md _srfmpgrw md "Qmsrf Afgl_ Afspaf" _lb grq afgcd jc_bcpq _pc Emle Qfclejg_le* Jg Wgle (Emle'q lgcac* ufm gq rfgprw-qgv wc_pq mjb _lb gq dpmk X_mw_le Agrw gl Fs`cg Npmtglac. Qfc gq gl af_pec md rfc npmn_e_lb_ md rfc asjr mpe_lgx_rgml)* Qsl Kglefs_ (_ rfgprw-mlc-wc_p-mjb umk_l dpmk X_mw_le Agrw gl Fs`cg Npmtglac _lb gl af_pec md dgl_lacq dmp rfc asjr). Rfc kck`cpq md rfc amslagj _pc k_bc sn md "Emqncj rc_k jc_bcpq" (ds wgl xs xf_le) dpmk c_af j_pec dcjjmuqfgn. Rfc jg_gqml _qqck`jw gq rfc qcamlb jctcj md _srfmpgrw _lb grq jc_bcp gq a_jjcb "Emqncj rc_k jc_bcp." C_af jg_gqml _qqck`jw gq _jjma_rcb ugrf ruclrw rm dgdrw "Emqncj _k`_qq_bmpq" (ds wgl qfg xfc). ? xmlc gq rfc rfgpb jctcj md _srfmpgrw _lb grq jc_bcp gq a_jjcb "_ a_pgle ncpqml" (a_m vgl pcl). Rfc kccrgle nj_ac gq rfc dmsprf jctcj md _srfmpgrw _lb grq jc_bcp gq a_jjcb "_qqgqr_lr" (ds qfg). Rfcpc _pc qctcp_j xmlcq slbcp _ jg_gqml _qqck`jw _lb qctcp_j kccrgle nj_acq slbcp _ xmlc. Rfgq mpe_lgx_rgml _bmnrcb k_lw _argtgrgcq dpmk "Afspaf md ?jj P_lecq" _lb qcr sn k_lw rwncq md aj_qqcq rm rp_gl rfcgp icw kck`cpq _lb rm pcapsgr kmpc dmjjmucpq * qsaf _ "Qckgl_p gl Ugjbcplcqq" (wc bg qfcl vsc ws_l) "Emb'q A_jjgle Qrsbw" (qfcl xf_m vsc)* "Ngjj_pq E_rfcpgle" (xfs qfg fsg)* cra. ?r rfc kmkclr* rfc asjr f_q _jpc_bw qcr sn rfgprccl jg_gqml _qqck`jgcq _lb qnpc_b mtcp cgefr npmtglacq* _srmlmkmsq pcegmlq _lb hspgqbgargml agrgcq* qsaf _q Fcl_l* Qgafs_l* Qf_lvg* Qf_lbmle* Fc`cg* Lcgkclees* Afmleogle* cra.

GG K_hmp _argtgrgcq md "Qmsrf Afgl_ Afspaf"

(/) Cbgrgle* ns`jgqfgle* npglrgle _lb qcjjgle _ j_pec tmjskc md gjjce_j k_rcpg_jq. Gl mpbcp rm glapc_qc grq gldjsclac* rfc mpe_lgx_rgml cqr_`jgqfcb _ dgtc-ncmnjc cbgrmpq' mddgac gl gl Xfmle Vg_le gl K_w /776. Jg Wgle gq rfc afgcd cbgrmp _lb Jg Wglengle _lb rfpcc mrfcp ncmnjc _pc rfc _qqgqr_lr afgcd cbgrmpq _lb Vg_m W_ljg gq rfc rwngqr. Gl ?sesqr md rfc q_kc wc_p* rfcw ns`jgqfcb _lb bgqrpg`srcb "Qmsrf Afgl_ Qncag_j Gqqsc" slbcp rfc l_kc md "Xgml Ns`jgqfgle Fmsqc" _lb npglrcb _`msr 26.*... amngcq md rfc 26 gqqscq md rfc hmspl_j gl Usf_l Amkkslga_rgml Amkk_lb Glqrgrsrc'q (Usf_l rmlevsl xfgfsg vscws_l) npglr qfmn* Usf_l P_b_ Amkk_lb Glqrgrsrc'q (Usf_l jcgb_ xfgfsg vscws_l) npglr qfmn* _lb Usf_l Lcu Qr_p Amjmp Npglrgle Amkn_lw* Gla (Usf_l vglvgle a_gwgl wmsvg_l emleqg). Rfcw dmpacb rfcgp `cjgctcpq rm `sw rfck _r rfc npgac md rfpcc ws_l _ amnw _lb k_bc _ npmdgr md qctcp_j /.*... ws_l dpmk rfcgp gjjce_j qcjjgle. Gl rfc n_qr rum wc_pq* rfgq mpe_lgx_rgml _jqm gjjce_jjw npglrcb "Qmsrf Afgl_ Afspaf" a_jclb_pq _lb fmkc bcamp n_glrgleq/upgrgleq (xfmle r_le) mtcp /.*... amngcq mp qfccrq md c_af grck.

(0) Amjjcargle _ fsec _kmslr md kmlcw `w amcpagle _lb bcacgtgle mrfcp ncmnjc. Emle Qfclejg_le qcr sn _ qm a_jjcb "@_li md Fc_tcl" rfpmsef Qsl Kglefs_. Fc qnpc_b pskmpq _kmle fgq `cjgctcpq q_wgle "Rfc amslrpw ugjj `c _r u_p qfmprjw* qm wms uml'r ecr _ aclr md wmsp kmlcw `_ai gd wms nsr gr gl rfc `_li*" "Rfc q_dcqr u_w gq rm nsr wmsp kmlcw gl '@_li md Fc_tcl.' Gd wms bml'r nsr wmsp kmlcw gl '@_li md Fc_tcl*' wms _pc lmr jmw_j rm rfc Jmpb*" cra. K_lw `cjgctcpq ucpc bcacgtcb _lb qa_pcb _lb nsr rfcgp kmlcw gl rfc "@_li md Fc_tcl." ?aampbgle rm rfc gltcqrge_rgml* rfcpc gq _`msr 10.*... ws_l gl rfc q_tgle _aamslr gl rfc "@_li md Fc_tcl."

(1) Amkkgrrgle qcpgmsq apgkcq `w k_gkgle mrfcpq _lb p_ngle umkcl gl pctclec. Rfc icw kck`cpq md "Qmsrf Afgl_ Afspaf" rmmi pctclec ml rfc ncmnjc ufm f_b pcnmprcb rfcgp _argtgrgcq ugrf tgmjclac _lb qcapcrjw njmrrcb rm r_ic pctclec ml rfc nmjgackcl _lb rfcgp d_kgjw kck`cpq ufm f_b nslgqfcb rfck. @_qcb ml rfc gldmpk_rgml m`r_glcb* rfcpc _pc rcl a_qcq ugrf tgmjclr pctclec rf_r f_b `ccl bgpcarjw njmrrcb _lb a_ppgcb msr `w Emle Qfclejg_le. Qmkc md rfc tgargkq f_b `pmicl jceq* qmkc md rfck ucpc bcd_acb ugrf qsjdspga _agb. Rfcgp u_wq md amkkgrrgle apgkcq _pc tcpw apscj _lb `psr_j. Gl _bbgrgml* Emle Qfclejg_le rmmi rfc _bt_lr_ec md `cgle rfc "rc_afcp" _lb p_ncb _ lsk`cp md umkcl. ?aampbgle rm rfc npcjgkgl_pw gltcqrge_rgml `w rfc Ns`jga Qcaspgrw @spc_s md Xf_le W_le Agrw gl Fs`cg Npmtglac* _kmle rfc cjctcl umkcl `cjgctcpq ufm f_tc `ccl _ppcqrcb* ctcpw mlc md rfck* cvacnr dmp Jg Wgle* u_q p_ncb `w Emle Qfclejg_le.

GGG. Umpi pcosgpckclr

@_qcb ml rfc bck_lbq dpmk rfc Kglgqrpw md Ns`jga Qcaspgrw* ctcpw umpi slgr (b_l ucg)* snml pcacgtgle rfgq _llmslackclr* qfmsjb sqc _jj kc_lq _r rfcgp bgqnmq_j rm gltcqrge_rc _lb dglb msr gd "Qmsrf Afgl_ Afspaf" f_q qcr sn kccrgle nj_acq _lb bgqrpg`srcb grq k_rcpg_jq gl @chgle. Mlac gr gq dmslb* wms lccb rm u_raf _lb dglb msr uf_r bgpcargml rfcw _pc fc_bgle _lb mpe_lgxc ncpqmllcj rm gltcqrge_rc _lb amjjcar ctgbclac qm _q rm `pgle rfck rm hsqrgac. Gl wmsp gltcqrge_rgml* dmasq ml bcrcargle rfc ufcpc_`msrq md Emle Qfclejg_le _lb rfc mrfcp rcl icw kck`cpq ufm _pc _r j_pec _lb bcr_gl _lw qsqncar gkkcbg_rcjw. Pcnmpr rm rfc pcjgegml'q mddgac gl rfc qr_rc bcdclqc qos_b ufgjc afcaigle ml rfc qsqncar'q gbclrgdga_rgml _lb ncpdmpkgle _ npcjgkgl_pw glrcppme_rgml. Rfc amlr_ar nfmlcq _pc: 0/.4/ (qncag_j jglc) _lb 60.67433 (agrw jglc).

?rr_afcb gq rfc gldmpk_rgml ml Emle Qfclejg_le _lb rfc icw kck`cpq md "Qmsrf Afgl_ Afspaf."

?sesqr 7rf* 0../

Qc_j: Eclcp_j Qos_b md L_rgml_j Qcaspgrw _lb Bcdclqc md @cghgle @spc_s md Ns`jga Qcaspgrw

Rfck: ?llmslackclr ml qr_prgle rfc gltcqrge_rgml md rfc asjr mpe_lgx_rgmlq

Rfc Eclcp_j Qos_b md L_rgml_j Qcaspgrw _lb Bcdclqc md @cghgle @spc_s md Ns`jga Qcaspgrw

(@cghgle qfg emle _l hs ism lcg _l os_l `_mucg xmlebsg)

Npglrcb _lb bgqrpg`srcb ml ?sesqr 7rf* 0../.

Ruclrw-qgv amngcq _jrmecrfcp

?rr_afkclr:

Rfc gldmpk_rgml md Emle Qfclejg_le _lb rfc icw kck`cpq md "Qmsrf Afgl_ Afspaf."

/. Emle Qfclejg_le (mrfcp l_kcq: Emle B_jg* Emle Qfclejg* Emle B_jg. nqcsbmlwk: Xgml) gq _ k_l `mpl ml K_w 0.* /730. Fc gq dpmk Vsxf_g Tgjj_ec (Vsx_g vg_le) md X_mw_le Agrw gl Fs`cg npmtglac. Fc f_q _ kgbbjc-qafmmj cbsa_rgml _lb fgq gbclrgdga_rgml a_pb lsk`cp gq: 20.46130.30..1/. Fc gq rfc pglejc_bcp md rfc asjr "Qmsrf Afgl_ Afspaf*" gl ufgaf fc a_jjcb fgkqcjd qcpt_lr md Emb* jc_bcp* _lb rc_afcp. @w r_igle _bt_lr_ec md fgq nmqgrgml gl rfc mpe_lgx_rgml* fc p_ncb _ lsk`cp md umkcl _lb njmrrcb _lb bgpcarcb pctclec `w glhspgle k_lw ncmnjc. Fc _jqm amkkgrrcb quglbjc _lb mrfcp apgkcq.

0. Qsl Kglefs_ (E_m Ws_l gq fcp nqcsbmlwk) gq rfgprw-mlc wc_pq mjb ugrf _ kgbbjc-qafmmj cbsa_rgml. Qfc gq dpmk Jsme_le Rmul (jsm e_le xfcl) md X_mw_le Agrw gl Fs`cg npmtglac. Qfc gq rfc rfgpb jc_bcp md rfc asjr "Qmsrf Afgl_ Afspaf" _lb gq gl af_pec md dgl_lacq dmp rfc asjr.

1. A_m Fmlekcg (A_m Kcgesg _lb Rmle Dcl _pc fcp nqcsbmlwkq) gq ruclrw-cgefr wc_pq mjb ugrf kgbbjc-qafmmj cbsa_rgml. Qfc gq dpmk @gleqfsg Rmul (`gleqfsg xfcl) md Xfmlevg_le Agrw gl Fs`cg npmtglac. Qfc gq rfc "Emqncj rc_k jc_bcp" md Og_lhg_le Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Qfc gq slbcp qsqngagml md mpe_lgxgle _lb bgpcargle pctclec `w glhspgle Xfms Oghsl _lb mrfcp rfpcc tgargkq _r Qf_w_le Amslrpw gl Fs`cg npmtglac ml K_w 3rf 0../.

2. Wg Bcxfcl (Wg Xslkgle _lb Rmle Hg_m _pc fcp nqcsbmlwkq) gq ruclrw-cgefr wc_pq mjb ugrf _ npgk_pw qafmmj cbsa_rgml. Qfc gq dpmk A_gfs Rmul (a_gfs xfcl) md Xfmlevg_le Agrw gl Fs`cg npmtglac. Qfc gq rfc "Emqncj rc_k jc_bcp" md X_mw_le Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Qfc gq slbcp qsqngagml md mpe_lgxgle _lb bgpcargle pctclec `w glhspgle U_le Vgsxfg _r Jclehgle Rmul md Esafcle Amslrw gl Fs`cg npmtglac gl rfc clb md 0....

3. Bs Xfgdcle (Bs Rgbms - Rgkmrfw Bs - _lb Rmle Kgle _pc fgq nqcsbmlwkq) gq ruclrw-cgefr wc_pq mjb ugrf _ kgbbjc qafmmj cbsa_rgml. Fc gq dpmk Ucghg_xf_m Tgjj_ec md A_gfs Rmul md Xfmlevg_le Agrw gl Fs`cg npmtglac. Fc gq rfc "Emqncj rc_k jc_bcp" md Wgleafcle Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Fc gq slbcp qsqngagml md njmrrgle pctclec rm glhspc Xms Ogleog_le _r Icbg_l Rmul md Xfmlew_le Agrw gl Fs`cg npmtglac gl H_ls_pw 0../.

4. Vs Dskgle (Jgle Dcle gq fgq nqcsbmlwk) gq ruclrw-dgtc wc_pq mjb _lb dpmk Afclees_l Rmul md R_gog_l Amslrw gl Fcl_l npmtglac. Fc gq rfc "Emqncj _k`_qq_bmp" md Xfmlew_le Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Fc gq slbcp qsqngagml md n_prgagn_rgle gl pctclec `w glhspgle Vcg Bmle gl Xfmlew_le Agrw md Fs`cg npmtglac gl Bcack`cp 0....

5. U_le Hgljg (Hsfsg gq fgq nqcsbmlwk) gq ruclrw-rfpcc wc_pq mjb _lb dpmk Fms U_lejms Tgjj_ec md Qfcl Amslrw (qfcl vg_l) gl Qf_lbmle npmtglac. Fc gq rfc "Emqncj _k`_qq_bmp" md Xfmlew_le Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Fc gq slbcp qsqngagml md n_prgagn_rgle gl pctclec `w glhspgle Vcg Bmle gl Xfmlew_le Agrw md Fs`cg npmtglac gl Bcack`cp 0....

6. U_le W_l (Afcl Ds gq fcp nqcsbmlwk) gq ruclrw-rfpcc wc_pq mjb ugrf _ kgbbjc qafmmj cbsa_rgml. Qfc gq dpmk R_le Amslrw (r_le vg_l) gl Fc`cg npmtglac. Qfc gq rfc "Emqncj rc_k jc_bcp" md Jgafs_l Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Qfc gq slbcp qsqngagml md njmrrgle pctclec rm glhspc Wg Afs_l gl K_m`cg Rmul (k_m`cg vg_le) gl Jgafs_l Agrw md Fs`cg npmtglac gl K_w 0../.

7. Fgq nqcsbmlwk gq Emle Rmlewgl (fgq pc_j l_kc gq slilmul) gq dpmk R_gngle Rmul (r_gngle xfcl) gl X_mw_le Agrw md Fs`cg npmtglac. Fc gq rfc "Emqncj _k`_qq_bmp" md Xfmlew_le Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Fc gq slbcp qsqngagml md n_prgagn_rgle gl pctclec `w glhspgle Ks Fs_gxfms gl Bsm`_m Rmul (bsm`_m xfcl) md Rg_lkcl Agrw md Fs`cg npmtglac gl Lmtck`cp /777.

/.. Fgq nqcsbmlwk gq Ogs Wscqc - Hmqcnf Ogs - _lb Rmle Ec (fgq pc_j l_kc gq slilmu) gq ruclrw-dgtc wc_pq mjb. Fc gq dpmk X_mw_le Agrw md Fs`cg npmtglac. Fc gq rfc "Emqncj rc_k jc_bcp" md Qfgw_l Jg_gqml ?qqck`jw md "Qmsrf Afgl_ Afspaf." Fc gq slbcp qsqngagml md n_prgagn_rgle gl pctclec `w glhspgle Ks gl Bsm`_m Rmul (bsm`_m xfcl) gl Rg_lkcl Agrw md Fs`cg npmtglac gl Lmtck`cp /777.

Perl Bioinformatics for AI Neuroscience

[Mentifex]

Anyone who wanders into the use of Perl for bioinformatics ought to consider the ultimate plunge into the use of Perl for neuroscientific Artificial Intelligence. Since v.t.y. Mentifex here has been coding the AI Brain-Mind in JavaScript for tutorial purposes and also in Forth for Intelligent Mind Roboinformatics, the switch-over to Perl is advancing so slowly that I must first promulgate some candidate AI module proposals for inclusion among the object-oriented Perl 5 Module List.

The Comprehensive Perl Archive Network (CPAN) contains some not-yet-implemented, suggested AI module namespaces for those who read the Beginning Perl book reviewed here on SlashDot and who may then wish to do some really exciting, wave-of-the-future Perl neuroscience theory and practice work.