FUCHS@embl.bitnet ("Rainer Fuchs ", EMBL) (02/01/90)
During the last month we have received quite a lot of new software submissions
to the EMBL File Server. Included you will find a list of all programs now
available from the server. For more information, send a mail message ( *no*
interactive message !) to NETSERV@EMBL, containing the lines:
HELP
HELP SOFTWARE
New programs:
CIP (DOS)
Clones (DOS)
ElBaMap (DOS)
FAST (with CHAMP database) (DOS)
Ligate (DOS)
ProNet (DOS)
MiniMM (Mac)
RefStack (Mac)
The GenBank Software Clearinghouse Catalog (kindly provided by GenBank).
Rainer Fuchs, Ph.D.
EMBL Data Library
fuchs@embl.bitnet
Directory of MS DOS Molecular Biology Software on EMBL File Server
------------------------------------------------------------------
To receive files from this directory use the command:
GET DOS_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename ALX3$.UUE
version 1.0
size 140 k
compressed PAK
ASCII conversion UUE
author Gotoh O.
description Alignment of three protein or DNA sequences
literatur J. Theor. Biol. 121 (1986), 327-337
source code -
sw requirements -
hw requirements -
filename CIP$.UUE
version -
size 65 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Calculation of reaction conditions for dephosphorylation
literatur -
source code -
sw requirements -
hw requirements -
filename CLONES$.UAA
version -
size 190 k
compressed PAK
ASCII conversion UUE (split)
author Jenson, H. B.
description Management of clones, strains, libraries etc. databases
(Part 1 of 2)
literatur BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CLONES$.UAB
version -
size 45 k
compressed PAK
ASCII conversion UUE (split)
author Jenson, H. B.
description Management of clones, strains, libraries etc. databases
(Part 2 of 2)
literatur BioTechniques 7 (1989), 590-592
source code -
sw requirements -
hw requirements -
filename CMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements CGA card
filename ELBAMAP.UUE
version 2.2
size 55 k
compressed PAK
ASCII conversion UUE
author King G. J.
description Management of electrophoresis banding patterns
literatur CABIOS 5 (1989), 313-317
source code -
sw requirements -
hw requirements EGA card
filename EMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements EGA card
filename EZ-FIT$.UUE
version 1.1
size 170 k
compressed PAK
ASCII conversion UUE
author Perella F. W.
description Calculation of enzyme and receptor kinetics
literatur Anal. Biochem. 174 (1989), 437-447
source code -
sw requirements -
hw requirements CGA card
filename FAST$.UUE
version -
size 195 k
compressed PAK
ASCII conversion UUE
author Facchiano, A.
description Protein structure analysis
literatur CABIOS 5 (1989), 299-303
source code -
sw requirements -
hw requirements -
filename GEL$.UUE
version 17.2.89
size 50 k
compressed PAK
ASCII conversion UUE
author Thompson J. R.
description Calculation of DNA restriction fragment sizes
literatur Anal. Biochem. 115 (81), 113-122
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename HMOLECUL.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description graphics output of PCFOLD result files
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code available as MOLECSRC.UUE
sw requirements -
hw requirements Hercules card
filename HYDRASC$.UUE
version 1
size 30 k
compressed PAK
ASCII conversion UUE
author Penttila T. J.
description Contour map for two polypeptide sequences.
Regions with similar hydropathic properties and second.
structure properties are plotted.
literatur CABIOS, in prep.
source code -
sw requirements MATLAB-PC
hw requirements Math. co-processor, >2M RAM
filename LIGATE$.UUE
version -
size 75 k
compressed PAK
ASCII conversion UUE
author Jenson, H. B.
description Calculation of reaction conditions for ligation
literatur BioTechniques 5 (1987), 729-730
source code -
sw requirements -
hw requirements -
filename MOLECSRC.UUE
version May 87
size 70 k
compressed PAK
ASCII conversion UUE
author Thompson J. R. (Cedergren R.)
description Source code for *MOLECUL.UUE
literatur Nucl. Acids Res. 10 (1982), 8351-8356
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename MOTIF$.UUE
version - (bug fix with plain ASCII sequences)
size 45 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Motif searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename OLIGO.UUE
version 1.0
size 105 k
compressed PAK
ASCII conversion UUE
author Beadles K.
description Oligo-directed single amino acid substitution
literatur -
source code -
sw requirements -
hw requirements -
filename PATTERN$.UUE
version -
size 55 k
compressed PAK
ASCII conversion UUE
author Giles I.
description Pattern searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements (Turbo C for recompiling)
hw requirements -
filename PCFOLD$.UUE
version 4.0
size 160 k
compressed PAK
ASCII conversion UUE
author Zuker M.
description RNA folding
literatur Meth. Enzymology 180 (1989), 262-288
source code Fortran, Asm
sw requirements (Compiler for recompiling)
hw requirements -
filename PLASMID.UUE
version 1.1
size 75 k
compressed PAK
ASCII conversion UUE
author Lipsick J.
description Plasmid drawing program (CGA card req.)
literatur -
source code Basic
sw requirements (Quickbasic for recompiling)
hw requirements CGA card
filename PRONET$.UUE
version 1.0
size 110 k
compressed PAK
ASCII conversion UUE
author Pascarella S.
description protein structure prediction with a neural network
literatur CABIOS 5 (1989), 319-320
source code Pascal
sw requirements (Turbo Pascal for recompiling)
hw requirements -
filename SDSE.UAA
version 2.0
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Oliver J. L.
description Simulation of DNA sequence evolution (Part 1 of 2)
literatur CABIOS 5 (1989), 47-50
source code -
sw requirements -
hw requirements -
filename SDSE.UAB
version 2.0
size 50 k
compressed PAK
ASCII conversion UUE (split)
author Oliver J. L.
description Simulation of DNA sequence evolution (Part 2 of 2)
literatur CABIOS 5 (1989), 47-50
source code -
sw requirements -
hw requirements -
filename SEQAIDFD.UAA
version 3.5
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Roufa D.
description DNA and protein sequence analysis package (Part 1 of 2)
literatur -
source code -
sw requirements -
hw requirements -
filename SEQAIDFD.UAB
version 3.5
size 185 k
compressed PAK
ASCII conversion UUE (split)
author Roufa D.
description DNA and protein sequence analysis package (Part 2 of 2)
literatur -
source code -
sw requirements -
hw requirements -
filename SIGSEQ$.UUE
version 1.0
size 60 k
compressed PAK
ASCII conversion UUE
author Popowicz A.M.
description Prediction of signal sequence cleavage site
literatur CABIOS 4 (1988), 405-406
source code C
sw requirements (Compiler for recompiling)
hw requirements -
filename TDALIGN$.UUE
version 1.61
size 120 k
compressed PAK
ASCII conversion UUE
author Davison D. (Thompson K.)
description Sequence alignment
literatur -
source code -
sw requirements -
hw requirements -
(b) Archiving/Decoding Software
filename UUEMBL.UUE
version -
size 35 k
compressed PAK
ASCII conversion UUE
author Fuchs R. (Dumas M.)
description UUEncoded form of UUD uudecoder and UUE uuencoder
literatur -
source code C
sw requirements -
hw requirements -
filename UUD.C
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description Source code for recommended uudecoder
literatur -
source code C
sw requirements Turbo C
hw requirements -
filename UUDECODE.PAS
version modified 4-Dec-1989
size 6 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Pascal
sw requirements Turbo Pascal
hw requirements -
filename UUD19.BAS
version -
size 5 k
compressed no
ASCII conversion no
author -
description Source code for bootstrap uudecoder
literatur -
source code Basic
sw requirements GWBasic
hw requirements -
Directory of Apple Macintosh Molecular Biology Software on EMBL File Server
---------------------------------------------------------------------------
To receive files from this directory use the command:
GET MAC_SOFTWARE:filename.ext
filename BUFSTACK.HQX
version 1.1
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Beynon R. J.
description Calculation of thermodynamically-corrected buffer recipes
literatur CABIOS 4 (1988), 487-490
source code -
sw requirements HyperCard
hw requirements -
filename DNAID.HQX
version 1.1
size 230 k
compressed StuffIt
ASCII conversion StuffIt
author Dardel F.
description DNA sequence editor with grep-like search routine
literatur CABIOS 4 (1988), 483-486
source code -
sw requirements -
hw requirements -
filename DOTTYPLOT.HQX
version 1.0c
size 210 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Dot-matrix comparison of DNA sequences
literatur -
source code Pascal source for sequence loading subroutine
sw requirements -
hw requirements -
filename ENZYMEKIN.HQX
version 1.0
size 105 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of enzyme kinetics
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename GELFRAG.HQX
version 1.4
size 145 k
compressed StuffIt
ASCII conversion StuffIt
author Gilbert D.
description Calculation of DNA restriction fragment sizes
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename MACDNA.HQX
version 2/88
size 65 k
compressed StuffIt
ASCII conversion StuffIt
author Schleif R.
description DNA sequence analysis, ported from IBM-PC
literatur -
source code -
sw requirements -
filename MATMETH.HQX
version 3.1
size 225 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Molecular biological protocols
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename MINIMM.HQX
version 4.0
size 210 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Molecular biological protocols (more HyperCard-like)
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename REFSTACK.HQX
version 2.0
size 145 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Management of literature references
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RRNA1.HQX
version 0.3
size 165 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 1 of 2)
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename RRNA2.HQX
version 0.3
size 120 k
compressed StuffIt
ASCII conversion StuffIt
author Brown J.
description Phylogeny of 16/18S rRNA (part 2 of 2)
literatur -
source code HyperTalk
sw requirements HyperCard
hw requirements -
filename THREE.HQX
version -
size 80 k
compressed StuffIt
ASCII conversion StuffIt
author Markiewicz P. (Johnson M.)
description Alignment of three protein sequences
literatur -
source code -
sw requirements -
hw requirements -
Directory of VAX Molecular Biology Software on EMBL File Server
---------------------------------------------------------------
To receive files from this directory use the command:
GET VAX_SOFTWARE:filename.ext
(a) Molecular Biology Software
filename BUGFIX_6_1.GCG
version -
size 9 k
compressed -
ASCII conversion -
author -
description Fixes for several bugs in GCG package v6.1
literatur -
source code -
sw requirements GCG package,Fortran compiler, C compiler
hw requirements -
filename GCGEMBL.UAA
version -
size 180 k
compressed ZOO
ASCII conversion UUE (split)
author Rice P.
description GCG extensions developed at EMBL (part 1 of 2)
literatur -
source code Fortran
sw requirements GCG package v5 or v6
hw requirements -
filename GCGEMBL.UAB
version -
size 165 k
compressed ZOO
ASCII conversion UUE (split)
author Rice P.
description GCG extensions developed at EMBL (part 2 of 2)
literatur -
source code Fortran
sw requirements GCG package v5 or v6
hw requirements -
filename MOTIF.UUE
version -
size 90 k
compressed ZOO
ASCII conversion UUE
author Giles I.
description Motif searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename PATTERN.UUE
version -
size 100 k
compressed ZOO
ASCII conversion UUE
author Giles I.
description Pattern searching program
literatur CABIOS 5 (1989), 227-232
source code C
sw requirements VAX C for recompiling
hw requirements -
filename SHELLS.GCG
version -
size 90 k
compressed -
ASCII conversion -
author Clark S.
description DCL shells for many GCG programs
literatur -
source code DCL, Fortran
sw requirements VAX Fortran
hw requirements -
(b) Decoding Software
filename UUD.C
version -
size 20 k
compressed no
ASCII conversion no
author Dumas M.
description C source code for UUD uudecoder
literatur -
source code C
sw requirements VAX C
hw requirements -
filename ZOO.UUE
version -
size 60 k
compressed no
ASCII conversion UUE
author Dhesi R.
description Archiving program
literatur -
source code -
sw requirements -
hw requirements -
(c) Other software
filename CD_ACCESS.TXT
version -
size 145 k
compressed -
ASCII conversion -
author Stockwell P.A.
description Driver software for ISO-formatted CD-ROMs
literatur -
source code Pascal
sw requirements VAX Pascal
hw requirements CD-ROM drive
General
-------
To receive any of these files use the command:
GET SOFTWARE:filename.ext
The GenBank Software Clearinghouse - Filename: GBCLEAR.CAT
A listing of programs and packages available for molecular biology
Software submission form v. ESW2.89 - Filename: SUBMISSION.SW
To facilitate software submission to the EMBL File Server.
BIOBIT - An independent newsletter by Rob Harper, Helsinki, SF.
(Disclaimer: the contents of these newsletters does not necessarily reflect
the opinions of anyone at EMBL)
Filenames: Contents:
BIOBIT.1 - Computer Viruses
BIOBIT.2 - BIONET
BIOBIT.3 - Introduction to TRICKLE
BIOBIT.4 - How to use RELAY
BIOBIT.5 - Introduction to FTP
BIOBIT.6 - Introduction to ARC and UUENCODE
BIOBIT.7 - Compression schemes
BIOBIT.8 - Current Contents on diskette
BIOBIT.9 - Introduction to EARN node names
BIOBIT.10 - Use of gateways from UK
BIOBIT.11 - EMBL Software File Server
BIOBIT.12 - Database function of LISTSERV