From 70ae10c7a9e674f50bb82270bfe924fc86211475 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Mon, 23 Sep 2024 10:57:16 +0100 Subject: [PATCH 1/3] blog: Summary of funded proposals 2024 Short summary on the call for proposals and research projects that were funded. --- _posts/2024-09-24-funded-proposals.md | 93 ++++++++++++++++++ .../2024-09-24-funded-proposals-faculty.png | Bin 0 -> 24451 bytes 2 files changed, 93 insertions(+) create mode 100644 _posts/2024-09-24-funded-proposals.md create mode 100644 assets/images/2024-09-24-funded-proposals-faculty.png diff --git a/_posts/2024-09-24-funded-proposals.md b/_posts/2024-09-24-funded-proposals.md new file mode 100644 index 00000000..f28dbd00 --- /dev/null +++ b/_posts/2024-09-24-funded-proposals.md @@ -0,0 +1,93 @@ +--- +layout: post +title: "RSE Supported Projects" +author: Neil Shephard +slug: 2024-09-24-funded-proposals +date: 2024-09-24 12:00:00 UTC +tags: rse "call for proposals" support +category: +link: +description: +social_image: +type: text +excerpt_separator: +--- + +Earlier this year the RSE team in Sheffield put a call out for proposals for researchers in the University of Sheffield to +[collaborate with the RSE][originalproposal] team. The successful applicants would receive dedicated support from an RSE +Team member at 50% FTE for a period of six months. + + + +A total of 26 applications were received from across the faculties of the University and the review panel which +consisted of nine RSEs had robust discussions about which to fund as the quality and proposed work was of a high +standard. + +![Distribution of applications by faculty](/assets/images/2024-09-24-funded-proposals-faculty.png) + +In the end the RSE team was able to fund support for three proposals and team members [Robert Chisholm][rob] and [Neil +Shephard][neil] are about to start work on two of the projects with the third postponed, with agreement, until a new RSE +who has been recruited starts later in the year. + +All work undertaken will be done with a view to adhering to the [FAIR for Research Software Principles][fair4rs] + +## SLAMSeq + +SLAMSeq is software developed within the [SubLab][sudlab] which is lead by [Dr Ian Subery's][ian] and performs sequence +alignment of variably spliced RNA sequences to assess degradation rates. Despite wide adoption of the technique the +current software is limited to only being run on a per-gene basis rather than per isoform basis and statistical +comparison of differences in decay rates are limited. The [Sudlab][sudlab] have addressed this deficiency by developing +an analysis pipeline with pre-processing performed in Python and statistical analysis undertaken in R. + +RSE support will be used to refactor the code into formal packages with a modular code structure and formal tests which +facilitate long-term maintenance and make extension easier and will make it straight-forward for users to +install. Translation of code into a single language will be considered as this would lower the barrier to uptake by +external users and documentation will be developed and deployed covering the API and the practical side of using the +software. + +## HYBIRD + +[HYBIRD][hybrid] is software developed by [Dr Alessandro Leonardi][alessandro] and his research group with the +Geo-Technical Engineering group and is written using C++. It combines the Discrete Element Method (DEM) and the Lattice +Boltzmann Method (LBM) to simulate complex particle-fluid interactions. These fluid-structure interactions have +allowed the investigation of the formation of granular fronts in free-surface flows, enhancing understanding of +particle-laden flow dynamics which have been successfully applied to key areas in environmental and geo-technical +engineering. + +Work will be undertaken by [Robert Chisholm][rob] to re-write the build system in [CMake][cmake] which will make it +possible to compile and run the code across multiple operating systems and free it from is current constraints of being +developed using outdated software. Profiling and optimisation will then be undertaken to hopefully remove the current +large memory requirements required when running simulations. The possibility of parallelising the modelling via GPU and +Cuda will also be investigated. + +## Polychron + +[Polychron][polychron] is prototype software developed by [Dr Bryony Moody][bryony] of the School of Mathematical and +Physical Sciences that facilitates the analysis and archiving of archaeological dating evidence. Written in Python the +prototype consists of a statistical algorithm (backend) and a GUI frontend to facilitate usage. + +Work will be undertaken by a new RSE who will be starting later in the year. The exact remit of the work to be +undertaken has not yet been finalised but the code base will benefit from restructuring into a Python package with +refactoring of the GUI to make it easier to maintain and extend and improved error detection. + +## Summary + +As the number of applications demonstrated, the demand for RSE support across all faculties within the University is +high and it was interesting to find out about the broad range of software projects being undertaken by different +research groups. We wish we could have supported more of these teams. + +If you are considering putting in a funding application that involves writing/developing/maintaining software +having dedicated RSE support can strengthen your proposal. If you would like to speak to the RSE team about support +please don't hesitate to get in touch by emailing [rse@sheffield.ac.uk](mailto:rse@sheffield.ac.uk). + +[alessandro]: https://www.sheffield.ac.uk/mac/people/civil-academic-staff/alessandro-leonardi +[bryony]: https://www.sheffield.ac.uk/mps/people/all-academic-staff/bryony-moody +[cmake]: https://cmake.org/ +[fair4rs]: https://rse.shef.ac.uk/training/fair4rs/ +[hybrid]: https://github.com/gnomeCreative/HYBIRD +[ian]: https://www.sheffield.ac.uk/biosciences/academic-staff/people/ian-sudbery +[neil]: https://rse.shef.ac.uk/contact/neil-shephard/ +[originalproposal]: originalproposal +[polychron]: https://github.com/bryonymoody/PolyChron +[rob]: https://rse.shef.ac.uk/contact/robert-chisholm/ +[sudlab]: https://www.sudlab.co.uk/team-1/ian-sudbery diff --git a/assets/images/2024-09-24-funded-proposals-faculty.png b/assets/images/2024-09-24-funded-proposals-faculty.png new file mode 100644 index 0000000000000000000000000000000000000000..50875071973b54e614558a30078ecc61bf2f7dab GIT binary patch literal 24451 zcmeHv2~d++*0upLDhjPMjk30)(u$B)RAddVv?8FQqO!ym1rz~U1B4`~t+WfE%_blu zN^3*}6dDi+iMW8Q35z0zBtQ&=Eg=vHAf zp7Y#${h*Wm(#6_~=gph9bl)$#56_#YVmEJ|^2>$F;5V;d7!J;xr^GpU;K&~E-+ATR z=aJt)AP^-bC1qvh`Sa(isHiMhumB2$E?l^9(V|6*7cW*-Rb8@V$!-fsU#>N{rZZt75F*P-X!C*iC z{PU(wn>KIWY-VP*Wy_YWTeoi8w$0q!eEat878VwkmX=mlR@T5|5C*9oK+}+(hJv|W!#HmxKeg!}G zfYYZ>dwF@CIdkUh*|Xl>-abA)zP`Ta&Ye4d{=A=`--Qbo{Qdm{0s;a9120~@7!(u~ z92^`H5)v938Wt879v+TFA|oOqA|oTCqM}eJRCIJS8jZ$aFjy=$CMM?6rAwDDU%qnX z%5T5@cJ=DjYuB#D#>W2s`|sDUU%zqV#?6~IZ{4~T7Z(>FAD@traQpV{J9qB<@y8#D ziHS)`Ny*8{DJdzbsi}AG-c3tOOHWVF$jG>N?_OqRW>!`f4u`|z@%QiFfAHWzc6Rok zfByOK;loFd9uWwH$B!T9hyym?boQ}gcKySlo%`uh5YhK9z* zMhb;OrBa)ln_F61T3cJ&+S)#R_|V?o{_*3-j*bo*jn>)ONvG2p30z;0pFe+Qv)R49y?uRs91f?yzkgt0U~q77XlRJbY5D3Q4 zu*S#7CnhF@Lg8e%|K#MPNF-{2c(D38W6k`v=Bv;D z_I=zYzfIc9G}rEUuxWSVkD7-z{f>|Samkf4y58HF-WlPg!{IvV^lj%_>FXRzhPTli zX@6$4`6s#q6Xp5Lw6u`Su`K2|ODe(?2>V)uWBiYq7Cvfy?mQ+>jIu!9Zhi+E?_c^Pa8tunYOx;_w@4As#+)d#&CV+`nvQpWV6^@e$&& zO3injn(t~gUzab9Tgv4-b*Tq*sk?QlkG?ckKtr!?$ER(_U*C>*w3umZQsXQRvNH>^ z(+IN52%c$p=~6X&V!V4|*7d|}W6w0Ix8sf9KpNjb9N$3v>t-5pL3XacE2m#qPXAr` zQ_@UBn-!D)9dwHZbjvd6U+ZTYTdMzS9@JMA;18VWd9N@kXv-hkwyxR8A5a*6lbWyU zfcEl~h%kk7RzUw!30u0zfoQ34;4S4(m&>pHw$@WmZadIq{yRK&y;@!nFSjpf))IXF zs$Z|W*2sMTn%?bT`|W3Ma#?aef$lMR?Dxy@f1}$rv?!OmcJs5F>%FmS5!n)-{q?R%t=|CE3Q669_H=Y9xM~0^Vj#d9pH|&2`H=29f{~(CCdj=xK z9#c=hpTFvUZU3tokleDk5rjJG=g?ngU{d?4HwbpV!R0^C0A<`xGZ1CBSa{r>fy%x2 zSAt-Xe$TXF1}w9wOF)cqbkgdbfy+a_*FdaYM^FusPktay|FmV7$F7};tyeANQzVGg z-_Je9zrQse?bR^&$;g`b#;U+lmQS$4=iD@{6@*jf56;L@Q8@dD|MLBfsrFet?W?@7yT1J?tK{Quc88B5qJSR`N%n9xxjmG z#L==K?reveO4d_&VetGW*KS@;S4Yv2dtn*hfsVAWwKM@+2V zn8E6`J@DN(a=xb`lXCkQwye?m@&M9{PFvuPny=H}46vA!$zB^07-)6ebCbBKn5_*B z)tnvXE(DxUvR6es7AUMIV7ao1;E~JCzCx>ZHJd7khsx|#+7@xvvP(3W@Wc6cC4d#f zqwc=4ADe2tt+YhQ{$hf^UDXJ0Kp%0#d)V1$yJDuO-84oi+c`&0>gmxNy-X)N8mxCxzU89Y&eBPfeG^exj$wIX_GNJlbzppbW7QJ3Q3g$TmaiQIltB zq65h>jKf)ElsBzbNOupgKneb`s<+quyCdAf12OHwR44&1j2?YnY-I5@L7*+|EDi@! zgdQIGIJ7t|xJ{O{(2Uz_mdbL$)iZR-i8y-JFBv_9UHF#FXn$pnXo?twxre1$|Xi$0t zWWy8;*jBa6X*S`M$Vj0^2Vx^`JD((WmMjt6q+97yJJ0LRH)CaDB|aG%rKzb6q{oi*fv!b3^hYsEeE(QD!^m*T~%?+13 z<5odKmA_?&RfCZii?CfW0hhmFqI;je4;07BDEvtnw(1|Q`^)QkVF`AVKG4`FoGnE2Jw26USe*o5xL`QH%^A8SXSSdJFwPYL{hwWVz{u6&Z%?}1 zNf%`DCn=Z`Pg_0e(^=F!al4|QERs<$NV9)1st$ex5OST3f`L zYr*p3lhv2W`P5agB&D73=Afd^^@U}JJO%H1kacH8ojlbV{*tlBXo9Dmw_d(W!8_{B zgbMSY?F1eBU;fbVgidzCiNiA`5{0n^xcu@Gm}P^pTyY>TP;?2JeN#WH!ff!gDD06L z7G=iNzooA&0iN1^;}*v2qa96qVk6fM;UvpFrP>?rN)B8sRa`)3L%lccevGT%Pk_Gf zYNiz#IuO%4f3B;{^>2_8o*R^N@TaJ=&SCc4>?kjs&rRub!IL6;`QM573VT4Mi#>@y z(rzny5XUQj@)T7LQdwVztjDbI1vba(E*YL3CYTd>meA0LUxU@tP&=XCdh;QJ;fTRc zpB$V?V=1E&x*1KEdi3jfxUdCMSr{E&BcSEh8#$527==2RXUgdsUq!+1_Cp1!bEBUR^-cS55vU+Q|86`KWaWPA1D4J^pI98!_+L6Z!P{^lZ;vAKnM+0C2D?uI_` z)8#vxM1-;f>0&Y_D z^{~NmQBSZ~lCT|bap|i}0dypj*j)h2qlG^so}S3`tKX`|+3=MZ~@E@1pHBR^B1pB&6A@HZ8lL{#9-nUc(O4y>PFr%Tcxf-JFOjZN#fjV&3Q{9 z;-2e-_k|^MV`~mFW~k?XH-L9g=P*3Kp;Be7N82a%#Fm-{5FC>nJ29Ku+1t{W{H3%~@lvZ~W(sg$2uBC(fIvyI#I809YQJ8|l-l z92HZ(Q3Y@<^0zCP&pB$VA7^Jv$s!{QD3t= zJ4&@utemAJ0{U?gAoxZm@=s6kV&Cg1g_%N~q@?M}LC%-UD!2`fTtcXLj%m{F=F!(u zBTR|ttqVEuxLsodskGD6bF+A&C%83-S*oZSD9Nh>nuyXuv%T4^@DO%8sldl2` zh!8Xz9042p(Sl}=f%fl^)!7LQ`RT;oW_$P(%u?ptnXQHnx;4z~4^;dweiiN!+I&;q z6Qx=nf+ccsR_9GqOBYaNwVn6iCa84Z)j4s~H0t`))*~aofsK@@t@7QlWZsfhKi{!y;NquUFN4XpXnnr8v`JB9~5kJnq3cAvlJT6bTsh6$7(CT*5Z#E*|n zQni>Byvc;hp{W9c$gUEr}hx*M{o0V-HZ`iM@q~lE3oJ+C$Ek>sr;Ys64 z3>P)5AHA~DVA4i|I?Q&xH~jV)RGoX63`TK0pOEb@YU!z9urv%g(1X7xn8>UT1Y~kmm_wgA-VQYv@;_9K|2f zt1u-NbZ(P2#b?xa*Hh@2DOF66|L}u#1v!0HnMLD;4Jx53IN(UrMnC6%l8_WU_6&Qb zy(Apw^WFDU71()>A7huqY$-=M$|16zP+wtA@}YPw=JehaepD*=7kW)e?i8vQ@v zoM+rv-LSz=1p}Ba4YtuXsG#An=k|`U7sM#3UWHn!7L;sTI9`RG7)RJf)5N%sl_B*m z#Qt~prdp3g$c#NEk}qN`%4K9b+5|TfGsd#7?*?}@XrIs}$G}Jhy5djG!Gf^teih=x z$frQexxCIov}{+O?UP~?2z~MaLNu$WAa-CuU0&1NZ_-yJNt0*6PwH;-oDfzdtdOuDnhF6>9mS=nq!ht6QC zw>0-wQ+a`I+2E=5t^t#iaRt8I9{-Axq-^!1Slf{mN>d%9)I9a1;(9ebQKz{>q$95n z$H*VoDj9$Az*U>1ofwma2)K(D3JekGRSP*qkI211qlU2StQOpOa{P{oI(IN3$qRun zhEg&}&)Mr4(Px}Q=Qdaa#iru@AJK@&t{Y3S^Mp@}vr{h^*o?;qk58#|h6Rc`JhC%g z^K2x4^{Z?|I@wMVz1VBV3@n9*^86QZu4#oeJ{`U_g1_19toCcDepErit%*)Kg{ zEAC^xxh|$PDQ_Ao+xk)s6I}~gj_j=FM~GLcRz}XRBh^#2b|YS9o*i8iUFdFwVog3g z0VI#w*VQzwh%;SZ<0MP9>-B8zd@H^mJY*CemxaVzUyDi6an>0o6(_j~&I6A?0_LdQDl~C|1y>{`!=I^)DYcV1zG^AXMHL5OFDiTS zv=L)0tsZ4fzdzkYKk5`+u%@B%v3e3N3j>VnD3^E3$4aM8YRV|FU&jqdD|0T>O?+eh zf;2+ixG4lSZm*6oL$OX-pk3?|$O8_S5rDW(fE1aUs&ns=!XzzEp@MvFUIIOO6l>h) z*<5|IbU63yL@d=Ak)h6!lsiHyu_p=pA_?%VQ9DHEnSIRV)G}2S&vTOV2b3(M5NXo= zU5V^YQA_};XDzhd(@NCj&mN_w>Yi%7g7Oeihcu&eh|8?sx+OHMw{?u`Be$GIXjZ^P zllS`rSJNkUC7PG$d1Od;V`v$s%nu$fDJfj_K2LXUy5~z+6JrvUh*;c!=5*Q@mvr+k zIpON!VCMymo2?dAs0A+MTr@Im#`PrzS}VEAVB#wIVzPBI_N;Aeo5L^?33Ysm!5HugKW~ zZS5=-mCg_4?#!G@UXWkC1rOU`fa7kTN^Vx|1%<=wg_RekCg^mY^_H!|u6WWWY37yd z=1DqLF2sP>cdBrY>c$ZLg$1|$`$+wX_WL6#pS6_EzGgnX=kf9i`*r&P4@A5Z?36GA z&P%t^(XkEXW}l>uI!q?Q&bNQM!_7nnEacQ0WMSp+XK4}P;wDQIfv$DK+^OiF3a}Cu zyLuu6JC;+q1PCvFL8usgc0%iTz(#`%Oo+m%TNC%Y3$Gbb07D(QSCKo)ip6}S^)Zf|H1GI+%dV2+;kSP)yLgT%6gre1iKgAE>Pljj)Yv*t5FvY zDFsNVqJ;DQ4tCC@#{>!{(Wj?(Da1zfI;0>(wg+*N0T(|r0U9I(_xQ%^9ieDuH1L@Q z#ft8mK!#=7F5B@iEB@Q~1DLnSo)%qzwi6~A??-$G^r&B$G}=ab5T_L=B_y`uR$Ntz zdO{&v;4@6Wk9gRfyJ;!svylkCS$bmJ%svC79$HhcmV(oD#0CK*4L}mY)RyWcd(y9< zoXQGNV?)6g2VIuLFOh8t%K|o}qW2I1*Q`iM1rFvKpLK|Y8Ljb7l~F%6CGt8VAbko) z4KCtj70O!QTAi}%L&!&8e!EXS+zbGr*x_`q=K!s47cZ(G++OF>F^JSRvdh@4#+#fG zC26@Q8B9sQj-$vY>r^H+8{uaM;mYW-+cAuYCox&0V}YWToZc%hM9I|!)f@4Y3~8A} zFS`+3+r~H&kk(kqdV_m~#k*^XMhVaQt8DmYRGu+1h7d6*?`|K)5Z#3ZzavcGQIZPt zlj zZ4W=1rKU7Rtuwfo(#PVc9SC#n z%9iL~-4cu=reC&$ty=Sl8L)^WOg3yq5OLwC$jQ1s?#FO$tV0I;HdE4NE8=`|9@fp| ztFm9RUb+y+-`(qJZHtiQx=$qY|LkYJ+#Y^r6p&U6`d4@qAJZ=%JYI%w=QA;+5x29$ z`Otd9RL9eJv(}*%o!qScG}#M@Mdx)!k0z*s zvs&j{+Qg;9@tv+87+{C-Kqh(NDx}9n641{B6lP{~hdj)yGLA#Unc}kxLV-t(DKS|` z%gN0ly*}#_+M2x*$6ZGdL`pAI*kZ`;t}s|Hq<9YZ5?1J@xkRTgreNdhNjpo(vP7Y- zh2W}A69OxKNEVF8+G5!P;cxAL(i;l{qLhXNUJVJ;`(Rzy6a#RZ#D>}*I2agpNGp24 zjVbBKEKT)!y`qWSv@}ovhI(MkJHmSv7)^&?9J?`P5Ep$mTEt_-v4H%vp8!~3urhjz8Lvh zkfB-uZ1DQve9k+Cs{WJ?+@Om+(a(t6#t2)?>N)6l_tp> zKky>#uxLra0C}5PQQJBQy00g}axJv2frPZcdwZ_|Tes#bMb*-Q4zlDXd@_Mih?Wkg zVuo?RI8NGUa8KIajkDG-0GMNu^%2orehlNibXi+iwnH^5_XCh)UxR&?1o8IX;HEV7 z0-6BakuZ5O^^cMkW@w;H*b102Rh7zFh&XJnxVtZ|26wz?iCGbwww$U{!-7lRmdZZI zVYlmJL#4{Hc8aGciws}SX>w5!e1>(a-vSaV0IO;M_$=CXIMVn~tJ zvO68{W9g&|W@eRn5Ol2`@VTHIciTy+d<@XRdb89`mvFe`6+o|VXm>5S>5TUT{k(%6 ze8QZ?Crb;!#4!QmrA;-fW+CX4*{aHxQN9uaZEtBDP|!*vhntz@G(sxRjA~HKGq*_@ z9z}>(0EKR_SP!`w&$HcQSD>2!`!qpdiM7cAW@csJu~><#GnXVBKVb)SPm)gpcMvi< zGfPEK$87{gzK77qTv=|OR{8*Exo1UMT3c_7>Z_!P&@ zQ(7#0q!Z&)_+W&K9Wc(PjI@HUng*yI^7dvXgV|&ri_arVA8KJIaS1@Mq!eC)oG|YP zQW4leinX;qkljz&fJIr$V2tQ08t9eM5Qy|WpDF$9;C){&QD&nzv*E&9Yu4qOaS6x1hSg^>{P1oX+FV3nVV`0ad3zi8zi08G?+dCLE{qS+ z#4T7$nFA1ex1mA5$d7>4#@?JddN(Z(zt0Zf#sDU3%!+CPgz8d(s{D+9?K1>G{VpxG VUywLtCErbd-yWyk`8!Wt{vXahwh{mU literal 0 HcmV?d00001 From e562d18492538ccbafd9a0ed7ae0089c2f681d82 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Mon, 23 Sep 2024 10:57:16 +0100 Subject: [PATCH 2/3] blog: Summary of funded proposals 2024 Short summary on the call for proposals and research projects that were funded. --- _posts/2024-09-24-funded-proposals.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/_posts/2024-09-24-funded-proposals.md b/_posts/2024-09-24-funded-proposals.md index f28dbd00..4f975772 100644 --- a/_posts/2024-09-24-funded-proposals.md +++ b/_posts/2024-09-24-funded-proposals.md @@ -25,7 +25,7 @@ standard. ![Distribution of applications by faculty](/assets/images/2024-09-24-funded-proposals-faculty.png) -In the end the RSE team was able to fund support for three proposals and team members [Robert Chisholm][rob] and [Neil +In the end the RSE team was able to fund support for three proposals and team members [Dr Robert Chisholm][rob] and [Neil Shephard][neil] are about to start work on two of the projects with the third postponed, with agreement, until a new RSE who has been recruited starts later in the year. @@ -54,11 +54,10 @@ allowed the investigation of the formation of granular fronts in free-surface fl particle-laden flow dynamics which have been successfully applied to key areas in environmental and geo-technical engineering. -Work will be undertaken by [Robert Chisholm][rob] to re-write the build system in [CMake][cmake] which will make it -possible to compile and run the code across multiple operating systems and free it from is current constraints of being -developed using outdated software. Profiling and optimisation will then be undertaken to hopefully remove the current -large memory requirements required when running simulations. The possibility of parallelising the modelling via GPU and -Cuda will also be investigated. +Work will be undertaken by [Dr Robert Chisholm][rob], a performance optimisation and GPU parallelisation specialist from +our team, to modernise HYBIRD's build system, address the limiting factors of its performance and enable it to take +advantage of GPU parallelisation. The broad objectives of this project are to reduce barriers to entry for new users and +to increase the performance to enable faster and larger research experiments. ## Polychron @@ -82,7 +81,6 @@ please don't hesitate to get in touch by emailing [rse@sheffield.ac.uk](mailto:r [alessandro]: https://www.sheffield.ac.uk/mac/people/civil-academic-staff/alessandro-leonardi [bryony]: https://www.sheffield.ac.uk/mps/people/all-academic-staff/bryony-moody -[cmake]: https://cmake.org/ [fair4rs]: https://rse.shef.ac.uk/training/fair4rs/ [hybrid]: https://github.com/gnomeCreative/HYBIRD [ian]: https://www.sheffield.ac.uk/biosciences/academic-staff/people/ian-sudbery From 9bf827151e82ce017c5831fcbab0fef43c20e8d5 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Wed, 25 Sep 2024 22:16:01 +0100 Subject: [PATCH 3/3] Address feedback from PIs --- _posts/2024-09-24-funded-proposals.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/_posts/2024-09-24-funded-proposals.md b/_posts/2024-09-24-funded-proposals.md index 4f975772..f59dad25 100644 --- a/_posts/2024-09-24-funded-proposals.md +++ b/_posts/2024-09-24-funded-proposals.md @@ -33,11 +33,12 @@ All work undertaken will be done with a view to adhering to the [FAIR for Resear ## SLAMSeq -SLAMSeq is software developed within the [SubLab][sudlab] which is lead by [Dr Ian Subery's][ian] and performs sequence -alignment of variably spliced RNA sequences to assess degradation rates. Despite wide adoption of the technique the -current software is limited to only being run on a per-gene basis rather than per isoform basis and statistical -comparison of differences in decay rates are limited. The [Sudlab][sudlab] have addressed this deficiency by developing -an analysis pipeline with pre-processing performed in Python and statistical analysis undertaken in R. +The [SubLab][sudlab], which is lead by [Dr Ian Subery][ian], have developed software to analyse the output of SLAMSeq +experiments which performs sequence alignment of variably spliced RNA sequences to assess degradation rates. Despite +wide adoption of the technique the current software is limited to only being run on a per-gene basis rather than per +isoform basis and statistical comparison of differences in decay rates are limited. The [Sudlab][sudlab] have addressed +this deficiency by developing an analysis pipeline with pre-processing performed in Python and statistical analysis +undertaken in R. RSE support will be used to refactor the code into formal packages with a modular code structure and formal tests which facilitate long-term maintenance and make extension easier and will make it straight-forward for users to