Friday, March 12, 2010
LIMS - laboratory information management system
http://en.wikipedia.org/wiki/Laboratory_information_management_system
description logics - dl, alc
Description logics
• Formalisms for expressing concepts, their attributes (or
associated roles), and the relationships between them.
• Can be regarded as providing a KR system based on a
structured representation of knowledge.
Description Logic: (p138) - Ch 9
Three types of non-logical symbols:
• atomic concepts:
Dog, Teenager, GraduateStudent
We include a distinguished concept: Thing
• roles: (all are atomic)
:Age, :Parent, :AreaOfStudy
• constants:
johnSmith, chair128
Four types of logical symbols:
• punctuation: [, ], (, )
• positive integers: 1, 2, 3, ...
• concept-forming operators: ALL, EXISTS, FILLS, AND
• connectives: =, =, and →
[AND Company
For example: [EXISTS 7 :Director]
[ALL :Manager [AND Woman
“a company with at least 7 directors,
whose managers are all women with [FILLS :Degree phD]]]
PhDs, and whose min salary is $24/hr” [FILLS :MinSalary $24.00/hour]]
([AND Surgeon Female] = Doctor) is not valid.
C= is subsumed-by
But it is entailed by a KB that contains
(Surgeon = [AND Specialist [FILLS :Specialty surgery]])
(Specialist C= Doctor)
computing subsumption, that is, determining
whether or not KB = (d subsumed-by e) - 'no negation of alpha query)
assumptions:
- KB is acyclic
- d is atomic, only appears once in LHS
- replace
Under these assumptions, it is sufficient to do the following:
• normalization: using the definitions in the KB, put d and e into a special
normal form, d′ and e′
• structure matching: determine if each part of e′ is matched by a part of d′.
- In other words, for every part of the more general concept,
there must be a corresponding part in the more specific one.
p153. [and person [fills :age 27]
computing satisfaction: To determine if KB = (c → e), we use the following procedure:
1. find the most specific concept d such that KB = (c → d)
2. determine whether or not KB = (d C= e), as before.
joe->person , canCorp, joe is manager of cancorp, manager of cancorp is canadian, so you get joe->canadian
computing classification:
- Positioning a new atom in a taxonomy is called classification
- wine example, Wine is at the top root node, then there's white-very-dry-bordeaux-wine
The Logic ALC
Main components:
• Concepts: classes of individuals
• Roles: binary relations between individuals
• Complex concepts using constructors
• Define terminology: TBox
• Give assertions: ABox
Examples:
• Concept names: Person, Female
• Role names: ParentOf, HasHusband
• Individual names: John, Mary
Assertion C(a) (in B&L it's a->C)
MotherWithoutDaughter = Mother ∀ParentOf.¬Female
(P erson M ale)(John)
A Tableaux Algorithm for ALC (Attributive Concept Language with Complements, more expressive DLs)
• Try to prove concept satisfiability by constructing a model.
• A tableau is a graph representing such a model.
• A set of tableaux expansion rules is used to construct the tableau.
• Either a model is constructed or there is an obvious contradiction.
• If tree T contains a clash the concept C is unsatisfiable.
Unfolded: expand every concept name occurring in C
• Formalisms for expressing concepts, their attributes (or
associated roles), and the relationships between them.
• Can be regarded as providing a KR system based on a
structured representation of knowledge.
Description Logic: (p138) - Ch 9
Three types of non-logical symbols:
• atomic concepts:
Dog, Teenager, GraduateStudent
We include a distinguished concept: Thing
• roles: (all are atomic)
:Age, :Parent, :AreaOfStudy
• constants:
johnSmith, chair128
Four types of logical symbols:
• punctuation: [, ], (, )
• positive integers: 1, 2, 3, ...
• concept-forming operators: ALL, EXISTS, FILLS, AND
• connectives: =, =, and →
[AND Company
For example: [EXISTS 7 :Director]
[ALL :Manager [AND Woman
“a company with at least 7 directors,
whose managers are all women with [FILLS :Degree phD]]]
PhDs, and whose min salary is $24/hr” [FILLS :MinSalary $24.00/hour]]
([AND Surgeon Female] = Doctor) is not valid.
C= is subsumed-by
But it is entailed by a KB that contains
(Surgeon = [AND Specialist [FILLS :Specialty surgery]])
(Specialist C= Doctor)
computing subsumption, that is, determining
whether or not KB = (d subsumed-by e) - 'no negation of alpha query)
assumptions:
- KB is acyclic
- d is atomic, only appears once in LHS
- replace
Under these assumptions, it is sufficient to do the following:
• normalization: using the definitions in the KB, put d and e into a special
normal form, d′ and e′
• structure matching: determine if each part of e′ is matched by a part of d′.
- In other words, for every part of the more general concept,
there must be a corresponding part in the more specific one.
p153. [and person [fills :age 27]
computing satisfaction: To determine if KB = (c → e), we use the following procedure:
1. find the most specific concept d such that KB = (c → d)
2. determine whether or not KB = (d C= e), as before.
joe->person , canCorp, joe is manager of cancorp, manager of cancorp is canadian, so you get joe->canadian
computing classification:
- Positioning a new atom in a taxonomy is called classification
- wine example, Wine is at the top root node, then there's white-very-dry-bordeaux-wine
The Logic ALC
Main components:
• Concepts: classes of individuals
• Roles: binary relations between individuals
• Complex concepts using constructors
• Define terminology: TBox
• Give assertions: ABox
Examples:
• Concept names: Person, Female
• Role names: ParentOf, HasHusband
• Individual names: John, Mary
Assertion C(a) (in B&L it's a->C)
MotherWithoutDaughter = Mother ∀ParentOf.¬Female
(P erson M ale)(John)
A Tableaux Algorithm for ALC (Attributive Concept Language with Complements, more expressive DLs)
• Try to prove concept satisfiability by constructing a model.
• A tableau is a graph representing such a model.
• A set of tableaux expansion rules is used to construct the tableau.
• Either a model is constructed or there is an obvious contradiction.
• If tree T contains a clash the concept C is unsatisfiable.
Unfolded: expand every concept name occurring in C
Thursday, March 11, 2010
Open Data
http://radar.oreilly.com/2010/03/truly-open-data.html
open source practices to making data available to the public
http://agbt.org/about.html
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks.
http://twitter.com/bffo
open source practices to making data available to the public
http://agbt.org/about.html
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks.
http://twitter.com/bffo
Hematology and Oncology
http://answers.google.com/answers/threadview?id=509511
Hematology-Oncology(Heme/Onc) usually refers to the department
that sees patients with blood and platelet disorders and cancers that
are treated with a non-surgical therapy, such as bone marrow
transplant, stem cell transplant, pheresis, or chemotherapy. (Think
?liquid? therapy when differentiating heme/onc from oncology) Types of
cancer typically seen in a heme/onc department would be leukemias,
lymphomas, Hodgkins, non-Hodgkins, multiple myelomas and immunological
disorders. So, an oncologist is not a hematologist, or vice versa. But
a hematologist oncologist is a hematologist that specializes in the
diseases mentioned above. A hematologist oncologist would not treat
operable cancers such as prostate cancer.
Oncology usually refers a department that sees cancers that require
surgical treatment such as ovarian cancers, throat and digestive
system cancers, thyroid cancer, etc. Patients would be seen by an
oncologist or a surgeon with experience in cancer surgery. Some
doctors have received special training, or have experience with a
certain kind of medicine, and may see and treat patients themselves
without referring them to a specialist.
Because disorders and diseases seen in heme/onc often overlap, it is
more effective to have hematologists working closely with oncologists.
Many patients see both ?heme? and ?onc? doctors during the course of
their therapy. A breast cancer patient, for example, may be treated
with a bone marrow transplant or stem cell transplant, and her
oncologist would work in conjunction with the hematologist. Another
benefit to doctors and patients is the heme/onc clinic is equipped
with special microscopes and often have their own lab, which enables
the doctors and medical technologists to make rapid diagnosis, or
monitor patients quickly and efficiently. Hematologists and
oncologists are well trained specialists that have the skills to
identify cells under the microscope that general practice doctors
often don?t posses.
Hematology-Oncology(Heme/Onc) usually refers to the department
that sees patients with blood and platelet disorders and cancers that
are treated with a non-surgical therapy, such as bone marrow
transplant, stem cell transplant, pheresis, or chemotherapy. (Think
?liquid? therapy when differentiating heme/onc from oncology) Types of
cancer typically seen in a heme/onc department would be leukemias,
lymphomas, Hodgkins, non-Hodgkins, multiple myelomas and immunological
disorders. So, an oncologist is not a hematologist, or vice versa. But
a hematologist oncologist is a hematologist that specializes in the
diseases mentioned above. A hematologist oncologist would not treat
operable cancers such as prostate cancer.
Oncology usually refers a department that sees cancers that require
surgical treatment such as ovarian cancers, throat and digestive
system cancers, thyroid cancer, etc. Patients would be seen by an
oncologist or a surgeon with experience in cancer surgery. Some
doctors have received special training, or have experience with a
certain kind of medicine, and may see and treat patients themselves
without referring them to a specialist.
Because disorders and diseases seen in heme/onc often overlap, it is
more effective to have hematologists working closely with oncologists.
Many patients see both ?heme? and ?onc? doctors during the course of
their therapy. A breast cancer patient, for example, may be treated
with a bone marrow transplant or stem cell transplant, and her
oncologist would work in conjunction with the hematologist. Another
benefit to doctors and patients is the heme/onc clinic is equipped
with special microscopes and often have their own lab, which enables
the doctors and medical technologists to make rapid diagnosis, or
monitor patients quickly and efficiently. Hematologists and
oncologists are well trained specialists that have the skills to
identify cells under the microscope that general practice doctors
often don?t posses.
Wednesday, March 10, 2010
Hallmarks of Cancer
http://teachercenter.insidecancer.org/browse/Hallmarks%20of%20Cancer/
Hallmarks of Cancer
o Image:Hallmarks, Overview
Hallmarks, Overview
Cancer is a disease that affects people of all nationalities and age groups and all cancers start with mutations in one cell.
o Image:Hallmarks, Growing uncontrollably
Hallmarks, Growing uncontrollably
Professor Robert Weinberg explains that cancer cells have to learn how to grow in the absence of growth stimulatory signals that normal cells require from their environment.
o Image:Hallmarks, Evading death
Hallmarks, Evading death
Professor Robert Weinberg discusses how cancer cells have to learn how to avoid the process of programmed cell death known as apoptosis carried out in normal cells.
o Image:Hallmarks, Processing nutrients
Hallmarks, Processing nutrients
Professor Robert Weinberg explains how cancer cells have to learn how to become angiogenic, that is to say attract blood vessels to grow into the tumor mass.
o Image:Hallmarks, Becoming immortal
Hallmarks, Becoming immortal
Professor Robert Weinberg explains how normal cells can only double a certain limited number of times; and cancer cells have to learn how to proliferate indefinitely, i.e, they have to become immortalized.
o Image:Hallmarks, Invading tissues
Hallmarks, Invading tissues
Professor Robert Weinberg, explains that cancer cells have to learn how to invade and metastasize.
o Image:Hallmarks, Avoiding detection
Hallmarks, Avoiding detection
Bruce Stillman, Ph.D. is president and chief executive officer of Cold Spring Harbor Laboratory, explains that there are two adaptive immune responses, and those immune responses adapt to changes in cells in our body whether they be by infection or other.
o Image:Hallmarks, Promoting mutations
Hallmarks, Promoting mutations
Bruce Stillman, Ph.D., president of Cold Spring Harbor Laboratory, explains that genomic instability is a characteristic of cancer cells.
Hallmarks of Cancer
o Image:Hallmarks, Overview
Hallmarks, Overview
Cancer is a disease that affects people of all nationalities and age groups and all cancers start with mutations in one cell.
o Image:Hallmarks, Growing uncontrollably
Hallmarks, Growing uncontrollably
Professor Robert Weinberg explains that cancer cells have to learn how to grow in the absence of growth stimulatory signals that normal cells require from their environment.
o Image:Hallmarks, Evading death
Hallmarks, Evading death
Professor Robert Weinberg discusses how cancer cells have to learn how to avoid the process of programmed cell death known as apoptosis carried out in normal cells.
o Image:Hallmarks, Processing nutrients
Hallmarks, Processing nutrients
Professor Robert Weinberg explains how cancer cells have to learn how to become angiogenic, that is to say attract blood vessels to grow into the tumor mass.
o Image:Hallmarks, Becoming immortal
Hallmarks, Becoming immortal
Professor Robert Weinberg explains how normal cells can only double a certain limited number of times; and cancer cells have to learn how to proliferate indefinitely, i.e, they have to become immortalized.
o Image:Hallmarks, Invading tissues
Hallmarks, Invading tissues
Professor Robert Weinberg, explains that cancer cells have to learn how to invade and metastasize.
o Image:Hallmarks, Avoiding detection
Hallmarks, Avoiding detection
Bruce Stillman, Ph.D. is president and chief executive officer of Cold Spring Harbor Laboratory, explains that there are two adaptive immune responses, and those immune responses adapt to changes in cells in our body whether they be by infection or other.
o Image:Hallmarks, Promoting mutations
Hallmarks, Promoting mutations
Bruce Stillman, Ph.D., president of Cold Spring Harbor Laboratory, explains that genomic instability is a characteristic of cancer cells.
P-glycoprotein
http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/current_month.html
they pump toxins away from the cell, including cancer drugs, so they make them less useful, and this so cancers produce more P-glycoproteins to do just this.
so we are now trying to find ways to block P-glycoprotein from ejecting the drugs from the cells.
they pump toxins away from the cell, including cancer drugs, so they make them less useful, and this so cancers produce more P-glycoproteins to do just this.
so we are now trying to find ways to block P-glycoprotein from ejecting the drugs from the cells.
Ouellette and Stein -- Changing of the guard
http://www.nature.com/nature/journal/v428/n6982/full/nj6982-584a.html
Blast in ubuntu
BLAST
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdb.html
Fasta -> DB
For nucleotide: formatdb -i input_db -p F -o T
For protein: formatdb -i input_db -p T -o T
----refp_db----
>gi|113722133|ref|NP_055861.3| probable helicase senataxin [Homo sapiens]
MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLI
NHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCVEALCRM
EQANCSFQVFDKHPGIYLFLVHPNEMVRRWAILTARNLGKVDRDDYYDLQEVLLCLFKVIELGLLESPDI
YTSSVLEKGKLILLPSHMYDTTNYKSYWLGICMLLTILEEQAMDSLLLGSDKQNDFMQSILHTMEREADD
DSVDPFWPALHCFMVILDRLGSKVWGQLMDPIVAFQTIINNASYNREIRHIRNSSVRTKLEPESYLDDMV
TCSQIVYNYNPEKTKKDSGWRTAICPDYCPNMYEEMETLASVLQSDIGQDMRVHNSTFLWFIPFVQSLMD
LKDLGVAYIAQVVNHLYSEVKEVLNQTDAVCDKVTEFFLLILVSVIELHRNKKCLHLLWVSSQQWVEAVV
KCAKLPTTAFTRSSEKSSGNCSKGTAMISSLSLHSMPSNSVQLAYVQLIRSLLKEGYQLGQQSLCKRFWD
KLNLFLRGNLSLGWQLTSQETHELQSCLKQIIRNIKFKAPPCNTFVDLTSACKISPASYNKEESEQMGKT
SRKDMHCLEASSPTFSKEPMKVQDSVLIKADNTIEGDNNEQNYIKDVKLEDHLLAGSCLKQSSKNIFTER
AEDQIKISTRKQKSVKEISSYTPKDCTSRNGPERGCDRGIIVSTRLLTDSSTDALEKVSTSNEDFSLKDD
ALAKTSKRKTKVQKDEICAKLSHVIKKQHRKSTLVDNTINLDENLTVSNIESFYSRKDTGVQKGDGFIHN
LSLDPSGVLDDKNGEQKSQNNVLPKEKQLKNEELVIFSFHENNCKIQEFHVDGKELIPFTEMTNASEKKS
SPFKDLMTVPESRDEEMSNSTSVIYSNLTREQAPDISPKSDTLTDSQIDRDLHKLSLLAQASVITFPSDS
PQNSSQLQRKVKEDKRCFTANQNNVGDTSRGQVIIISDSDDDDDERILSLEKLTKQDKICLEREHPEQHV
STVNSKEEKNPVKEEKTETLFQFEESDSQCFEFESSSEVFSVWQDHPDDNNSVQDGEKKCLAPIANTTNG
QGCTDYVSEVVKKGAEGIEEHTRPRSISVEEFCEIEVKKPKRKRSEKPMAEDPVRPSSSVRNEGQSDTNK
RDLVGNDFKSIDRRTSTPNSRIQRATTVSQKKSSKLCTCTEPIRKVPVSKTPKKTHSDAKKGQNRSSNYL
SCRTTPAIVPPKKFRQCPEPTSTAEKLGLKKGPRKAYELSQRSLDYVAQLRDHGKTVGVVDTRKKTKLIS
PQNLSVRNNKKLLTSQELQMQRQIRPKSQKNRRRLSDCESTDVKRAGSHTAQNSDIFVPESDRSDYNCTG
GTEVLANSNRKQLIKCMPSEPETIKAKHGSPATDDACPLNQCDSVVLNGTVPTNEVIVSTSEDPLGGGDP
TARHIEMAALKEGEPDSSSDAEEDNLFLTQNDPEDMDLCSQMENDNYKLIELIHGKDTVEVEEDSVSRPQ
LESLSGTKCKYKDCLETTKNQGEYCPKHSEVKAADEDVFRKPGLPPPASKPLRPTTKIFSSKSTSRIAGL
SKSLETSSALSPSLKNKSKGIQSILKVPQPVPLIAQKPVGEMKNSCNVLHPQSPNNSNRQGCKVPFGESK
YFPSSSPVNILLSSQSVSDTFVKEVLKWKYEMFLNFGQCGPPASLCQSISRPVPVRFHNYGDYFNVFFPL
MVLNTFETVAQEWLNSPNRENFYQLQVRKFPADYIKYWEFAVYLEECELAKQLYPKENDLVFLAPERINE
EKKDTERNDIQDLHEYHSGYVHKFRRTSVMRNGKTECYLSIQTQENFPANLNELVNCIVISSLVTTQRKL
KAMSLLGSRNQLARAVLNPNPMDFCTKDLLTTTSERIIAYLRDFNEDQKKAIETAYAMVKHSPSVAKICL
IHGPPGTGKSKTIVGLLYRLLTENQRKGHSDENSNAKIKQNRVLVCAPSNAAVDELMKKIILEFKEKCKD
KKNPLGNCGDINLVRLGPEKSINSEVLKFSLDSQVNHRMKKELPSHVQAMHKRKEFLDYQLDELSRQRAL
CRGGREIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHIICCTLSTSGGLLLESAFRGQ
GGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRLLEEN
VEHNMISRLPILQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDWPFQPYLVFDVGDGSERRD
NDSYINVQEIKLVMEIIKLIKDKRKDVSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQGR
QKDCVIVTCVRANSIQGSIGFLASLQRLNVTITRAKYSLFILGHLRTLMENQHWNQLIQDAQKRGAIIKT
CDKNYRHDAVKILKLKPVLQRSLTHPPTIAPEGSRPQGGLPSSKLDSGFAKTSVAASLYHTPSDSKEITL
TVTSKDPERPPVHDQLQDPRLLKRMGIEVKGGIFLWDPQPSSPQHPGATPPTGEPGFPVVHQDLSHIQQP
AAVVAALSSHKPPVRGEPPAASPEASTCQSKCDDPEEELCHRREARAFSEGEQEKCGSETHHTRRNSRWD
KRTLEQEDSSSKKRKLL
>gi|187233964|gb|ACD01221.1| TP53 [Homo sapiens]
RAMAIYKQSQHMTEVVRRCPTNERCSDSDGLAPPQHLIR
>gi|119395734|ref|NP_000050.2| breast cancer type 2 susceptibility protein [Homo sapiens]
MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPS
YNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCPLLNSCLS
ESPVVLQCTHVTPQRDKSVVCGSLFHTPKFVKGRQTPKHISESLGAEVDPDMSWSSSLATPPTLSSTVLI
VRNEEASETVFPHDTTANVKSYFSNHDESLKKNDRFIASVTDSENTNQREAASHGFGKTSGNSFKVNSCK
DHIGKSMPNVLEDEVYETVVDTSEEDSFSLCFSKCRTKNLQKVRTSKTRKKIFHEANADECEKSKNQVKE
KYSFVSEVEPNDTDPLDSNVANQKPFESGSDKISKEVVPSLACEWSQLTLSGLNGAQMEKIPLLHISSCD
QNISEKDLLDTENKRKKDFLTSENSLPRISSLPKSEKPLNEETVVNKRDEEQHLESHTDCILAVKQAISG
TSPVASSFQGIKKSIFRIRESPKETFNASFSGHMTDPNFKKETEASESGLEIHTVCSQKEDSLCPNLIDN
GSWPATTTQNSVALKNAGLISTLKKKTNKFIYAIHDETSYKGKKIPKDQKSELINCSAQFEANAFEAPLT
FANADSGLLHSSVKRSCSQNDSEEPTLSLTSSFGTILRKCSRNETCSNNTVISQDLDYKEAKCNKEKLQL
FITPEADSLSCLQEGQCENDPKSKKVSDIKEEVLAAACHPVQHSKVEYSDTDFQSQKSLLYDHENASTLI
LTPTSKDVLSNLVMISRGKESYKMSDKLKGNNYESDVELTKNIPMEKNQDVCALNENYKNVELLPPEKYM
RVASPSRKVQFNQNTNLRVIQKNQEETTSISKITVNPDSEELFSDNENNFVFQVANERNNLALGNTKELH
ETDLTCVNEPIFKNSTMVLYGDTGDKQATQVSIKKDLVYVLAEENKNSVKQHIKMTLGQDLKSDISLNID
KIPEKNNDYMNKWAGLLGPISNHSFGGSFRTASNKEIKLSEHNIKKSKMFFKDIEEQYPTSLACVEIVNT
LALDNQKKLSKPQSINTVSAHLQSSVVVSDCKNSHITPQMLFSKQDFNSNHNLTPSQKAEITELSTILEE
SGSQFEFTQFRKPSYILQKSTFEVPENQMTILKTTSEECRDADLHVIMNAPSIGQVDSSKQFEGTVEIKR
KFAGLLKNDCNKSASGYLTDENEVGFRGFYSAHGTKLNVSTEALQKAVKLFSDIENISEETSAEVHPISL
SSSKCHDSVVSMFKIENHNDKTVSEKNNKCQLILQNNIEMTTGTFVEEITENYKRNTENEDNKYTAASRN
SHNLEFDGSDSSKNDTVCIHKDETDLLFTDQHNICLKLSGQFMKEGNTQIKEDLSDLTFLEVAKAQEACH
GNTSNKEQLTATKTEQNIKDFETSDTFFQTASGKNISVAKESFNKIVNFFDQKPEELHNFSLNSELHSDI
RKNKMDILSYEETDIVKHKILKESVPVGTGNQLVTFQGQPERDEKIKEPTLLGFHTASGKKVKIAKESLD
KVKNLFDEKEQGTSEITSFSHQWAKTLKYREACKDLELACETIEITAAPKCKEMQNSLNNDKNLVSIETV
VPPKLLSDNLCRQTENLKTSKSIFLKVKVHENVEKETAKSPATCYTNQSPYSVIENSALAFYTSCSRKTS
VSQTSLLEAKKWLREGIFDGQPERINTADYVGNYLYENNSNSTIAENDKNHLSEKQDTYLSNSSMSNSYS
YHSDEVYNDSGYLSKNKLDSGIEPVLKNVEDQKNTSFSKVISNVKDANAYPQTVNEDICVEELVTSSSPC
KNKNAAIKLSISNSNNFEVGPPAFRIASGKIVCVSHETIKKVKDIFTDSFSKVIKENNENKSKICQTKIM
AGCYEALDDSEDILHNSLDNDECSTHSHKVFADIQSEEILQHNQNMSGLEKVSKISPCDVSLETSDICKC
SIGKLHKSVSSANTCGIFSTASGKSVQVSDASLQNARQVFSEIEDSTKQVFSKVLFKSNEHSDQLTREEN
TAIRTPEHLISQKGFSYNVVNSSAFSGFSTASGKQVSILESSLHKVKGVLEEFDLIRTEHSLHYSPTSRQ
NVSKILPRVDKRNPEHCVNSEMEKTCSKEFKLSNNLNVEGGSSENNHSIKVSPYLSQFQQDKQQLVLGTK
VSLVENIHVLGKEQASPKNVKMEIGKTETFSDVPVKTNIEVCSTYSKDSENYFETEAVEIAKAFMEDDEL
TDSKLPSHATHSLFTCPENEEMVLSNSRIGKRRGEPLILVGEPSIKRNLLNEFDRIIENQEKSLKASKST
PDGTIKDRRLFMHHVSLEPITCVPFRTTKERQEIQNPNFTAPGQEFLSKSHLYEHLTLEKSSSNLAVSGH
PFYQVSATRNEKMRHLITTGRPTKVFVPPFKTKSHFHRVEQCVRNINLEENRQKQNIDGHGSDDSKNKIN
DNEIHQFNKNNSNQAAAVTFTKCEEEPLDLITSLQNARDIQDMRIKKKQRQRVFPQPGSLYLAKTSTLPR
ISLKAAVGGQVPSACSHKQLYTYGVSKHCIKINSKNAESFQFHTEDYFGKESLWTGKGIQLADGGWLIPS
NDGKAGKEEFYRALCDTPGVDPKLISRIWVYNHYRWIIWKLAAMECAFPKEFANRCLSPERVLLQLKYRY
DTEIDRSRRSAIKKIMERDDTAAKTLVLCVSDIISLSANISETSSNKTSSADTQKVAIIELTDGWYAVKA
QLDPPLLAVLKNGRLTVGQKIILHGAELVGSPDACTPLEAPESLMLKISANSTRPARWYTKLGFFPDPRP
FPLPLSSLFSDGGNVGCVDVIIQRAYPIQWMEKTSSGLYIFRNEREEEKEAAKYVEAQQKRLEALFTKIQ
EEFEEHEENTTKPYLPSRALTRQQVRALQDGAELYEAVKNAADPAYLEGYFSEEQLRALNNHRQMLNDKK
QAQIQLEIRKAMESAEQKEQGLSRDVTTVWKLRIVSYSKKEKDSVILSIWRPSSDLYSLLTEGKRYRIYH
LATSKSKSKSERANIQLAATKKTQYQQLPVSDEILFQIYQPREPLHFSKFLDPDFQPSCSEVDLIGFVVS
VVKKTGLAPFVYLSDECYNLLAIKFWIDLNEDIIKPHMLIAASNLQWRPESKSGLLTLFAGDFSVFSASP
KEGHFQETFNKMKNTVENIDILCNEAENKLMHILHANDPKWSTPTKDCTSGPYTAQIIPGTGNKLLMSSP
NCEIYYQSPLSLCMAKRKSVSTPVSAQMTSKSCKGEKEIDDQKNCKKRRALDFLSRLPLPPPVSPICTFV
SPAAQKAFQPPRSCGTKYETPIKKKELNSPQMTPFKKFNEISLLESNSIADEELALINTQALLSGSTGEK
QFISVSESTRTAPTSSEDYLRLKRRCTTSLIKEQESSQASTEECEKNKQDTITTKKYI
----refp_db-----
$ formatdb -i refp_db -p T -o T
----tp53.fa-----
>gi|187233964|gb|ACD01221.1| TP53 [Homo sapiens]
RAMAIYKQSQHMTEVVRRCPTNERCSDSDGLAPPQHLIR
----tp53.fa-----
$ blastall -p blastp -i tp53.fa -d refp_db
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdb.html
Fasta -> DB
For nucleotide: formatdb -i input_db -p F -o T
For protein: formatdb -i input_db -p T -o T
----refp_db----
>gi|113722133|ref|NP_055861.3| probable helicase senataxin [Homo sapiens]
MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEVLWELETLRLI
NHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKYPYLLLHERVNELCVEALCRM
EQANCSFQVFDKHPGIYLFLVHPNEMVRRWAILTARNLGKVDRDDYYDLQEVLLCLFKVIELGLLESPDI
YTSSVLEKGKLILLPSHMYDTTNYKSYWLGICMLLTILEEQAMDSLLLGSDKQNDFMQSILHTMEREADD
DSVDPFWPALHCFMVILDRLGSKVWGQLMDPIVAFQTIINNASYNREIRHIRNSSVRTKLEPESYLDDMV
TCSQIVYNYNPEKTKKDSGWRTAICPDYCPNMYEEMETLASVLQSDIGQDMRVHNSTFLWFIPFVQSLMD
LKDLGVAYIAQVVNHLYSEVKEVLNQTDAVCDKVTEFFLLILVSVIELHRNKKCLHLLWVSSQQWVEAVV
KCAKLPTTAFTRSSEKSSGNCSKGTAMISSLSLHSMPSNSVQLAYVQLIRSLLKEGYQLGQQSLCKRFWD
KLNLFLRGNLSLGWQLTSQETHELQSCLKQIIRNIKFKAPPCNTFVDLTSACKISPASYNKEESEQMGKT
SRKDMHCLEASSPTFSKEPMKVQDSVLIKADNTIEGDNNEQNYIKDVKLEDHLLAGSCLKQSSKNIFTER
AEDQIKISTRKQKSVKEISSYTPKDCTSRNGPERGCDRGIIVSTRLLTDSSTDALEKVSTSNEDFSLKDD
ALAKTSKRKTKVQKDEICAKLSHVIKKQHRKSTLVDNTINLDENLTVSNIESFYSRKDTGVQKGDGFIHN
LSLDPSGVLDDKNGEQKSQNNVLPKEKQLKNEELVIFSFHENNCKIQEFHVDGKELIPFTEMTNASEKKS
SPFKDLMTVPESRDEEMSNSTSVIYSNLTREQAPDISPKSDTLTDSQIDRDLHKLSLLAQASVITFPSDS
PQNSSQLQRKVKEDKRCFTANQNNVGDTSRGQVIIISDSDDDDDERILSLEKLTKQDKICLEREHPEQHV
STVNSKEEKNPVKEEKTETLFQFEESDSQCFEFESSSEVFSVWQDHPDDNNSVQDGEKKCLAPIANTTNG
QGCTDYVSEVVKKGAEGIEEHTRPRSISVEEFCEIEVKKPKRKRSEKPMAEDPVRPSSSVRNEGQSDTNK
RDLVGNDFKSIDRRTSTPNSRIQRATTVSQKKSSKLCTCTEPIRKVPVSKTPKKTHSDAKKGQNRSSNYL
SCRTTPAIVPPKKFRQCPEPTSTAEKLGLKKGPRKAYELSQRSLDYVAQLRDHGKTVGVVDTRKKTKLIS
PQNLSVRNNKKLLTSQELQMQRQIRPKSQKNRRRLSDCESTDVKRAGSHTAQNSDIFVPESDRSDYNCTG
GTEVLANSNRKQLIKCMPSEPETIKAKHGSPATDDACPLNQCDSVVLNGTVPTNEVIVSTSEDPLGGGDP
TARHIEMAALKEGEPDSSSDAEEDNLFLTQNDPEDMDLCSQMENDNYKLIELIHGKDTVEVEEDSVSRPQ
LESLSGTKCKYKDCLETTKNQGEYCPKHSEVKAADEDVFRKPGLPPPASKPLRPTTKIFSSKSTSRIAGL
SKSLETSSALSPSLKNKSKGIQSILKVPQPVPLIAQKPVGEMKNSCNVLHPQSPNNSNRQGCKVPFGESK
YFPSSSPVNILLSSQSVSDTFVKEVLKWKYEMFLNFGQCGPPASLCQSISRPVPVRFHNYGDYFNVFFPL
MVLNTFETVAQEWLNSPNRENFYQLQVRKFPADYIKYWEFAVYLEECELAKQLYPKENDLVFLAPERINE
EKKDTERNDIQDLHEYHSGYVHKFRRTSVMRNGKTECYLSIQTQENFPANLNELVNCIVISSLVTTQRKL
KAMSLLGSRNQLARAVLNPNPMDFCTKDLLTTTSERIIAYLRDFNEDQKKAIETAYAMVKHSPSVAKICL
IHGPPGTGKSKTIVGLLYRLLTENQRKGHSDENSNAKIKQNRVLVCAPSNAAVDELMKKIILEFKEKCKD
KKNPLGNCGDINLVRLGPEKSINSEVLKFSLDSQVNHRMKKELPSHVQAMHKRKEFLDYQLDELSRQRAL
CRGGREIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHIICCTLSTSGGLLLESAFRGQ
GGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISMKAQEYGYDQSMMARFCRLLEEN
VEHNMISRLPILQLTVQYRMHPDICLFPSNYVYNRNLKTNRQTEAIRCSSDWPFQPYLVFDVGDGSERRD
NDSYINVQEIKLVMEIIKLIKDKRKDVSFRNIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQGR
QKDCVIVTCVRANSIQGSIGFLASLQRLNVTITRAKYSLFILGHLRTLMENQHWNQLIQDAQKRGAIIKT
CDKNYRHDAVKILKLKPVLQRSLTHPPTIAPEGSRPQGGLPSSKLDSGFAKTSVAASLYHTPSDSKEITL
TVTSKDPERPPVHDQLQDPRLLKRMGIEVKGGIFLWDPQPSSPQHPGATPPTGEPGFPVVHQDLSHIQQP
AAVVAALSSHKPPVRGEPPAASPEASTCQSKCDDPEEELCHRREARAFSEGEQEKCGSETHHTRRNSRWD
KRTLEQEDSSSKKRKLL
>gi|187233964|gb|ACD01221.1| TP53 [Homo sapiens]
RAMAIYKQSQHMTEVVRRCPTNERCSDSDGLAPPQHLIR
>gi|119395734|ref|NP_000050.2| breast cancer type 2 susceptibility protein [Homo sapiens]
MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPS
YNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCPLLNSCLS
ESPVVLQCTHVTPQRDKSVVCGSLFHTPKFVKGRQTPKHISESLGAEVDPDMSWSSSLATPPTLSSTVLI
VRNEEASETVFPHDTTANVKSYFSNHDESLKKNDRFIASVTDSENTNQREAASHGFGKTSGNSFKVNSCK
DHIGKSMPNVLEDEVYETVVDTSEEDSFSLCFSKCRTKNLQKVRTSKTRKKIFHEANADECEKSKNQVKE
KYSFVSEVEPNDTDPLDSNVANQKPFESGSDKISKEVVPSLACEWSQLTLSGLNGAQMEKIPLLHISSCD
QNISEKDLLDTENKRKKDFLTSENSLPRISSLPKSEKPLNEETVVNKRDEEQHLESHTDCILAVKQAISG
TSPVASSFQGIKKSIFRIRESPKETFNASFSGHMTDPNFKKETEASESGLEIHTVCSQKEDSLCPNLIDN
GSWPATTTQNSVALKNAGLISTLKKKTNKFIYAIHDETSYKGKKIPKDQKSELINCSAQFEANAFEAPLT
FANADSGLLHSSVKRSCSQNDSEEPTLSLTSSFGTILRKCSRNETCSNNTVISQDLDYKEAKCNKEKLQL
FITPEADSLSCLQEGQCENDPKSKKVSDIKEEVLAAACHPVQHSKVEYSDTDFQSQKSLLYDHENASTLI
LTPTSKDVLSNLVMISRGKESYKMSDKLKGNNYESDVELTKNIPMEKNQDVCALNENYKNVELLPPEKYM
RVASPSRKVQFNQNTNLRVIQKNQEETTSISKITVNPDSEELFSDNENNFVFQVANERNNLALGNTKELH
ETDLTCVNEPIFKNSTMVLYGDTGDKQATQVSIKKDLVYVLAEENKNSVKQHIKMTLGQDLKSDISLNID
KIPEKNNDYMNKWAGLLGPISNHSFGGSFRTASNKEIKLSEHNIKKSKMFFKDIEEQYPTSLACVEIVNT
LALDNQKKLSKPQSINTVSAHLQSSVVVSDCKNSHITPQMLFSKQDFNSNHNLTPSQKAEITELSTILEE
SGSQFEFTQFRKPSYILQKSTFEVPENQMTILKTTSEECRDADLHVIMNAPSIGQVDSSKQFEGTVEIKR
KFAGLLKNDCNKSASGYLTDENEVGFRGFYSAHGTKLNVSTEALQKAVKLFSDIENISEETSAEVHPISL
SSSKCHDSVVSMFKIENHNDKTVSEKNNKCQLILQNNIEMTTGTFVEEITENYKRNTENEDNKYTAASRN
SHNLEFDGSDSSKNDTVCIHKDETDLLFTDQHNICLKLSGQFMKEGNTQIKEDLSDLTFLEVAKAQEACH
GNTSNKEQLTATKTEQNIKDFETSDTFFQTASGKNISVAKESFNKIVNFFDQKPEELHNFSLNSELHSDI
RKNKMDILSYEETDIVKHKILKESVPVGTGNQLVTFQGQPERDEKIKEPTLLGFHTASGKKVKIAKESLD
KVKNLFDEKEQGTSEITSFSHQWAKTLKYREACKDLELACETIEITAAPKCKEMQNSLNNDKNLVSIETV
VPPKLLSDNLCRQTENLKTSKSIFLKVKVHENVEKETAKSPATCYTNQSPYSVIENSALAFYTSCSRKTS
VSQTSLLEAKKWLREGIFDGQPERINTADYVGNYLYENNSNSTIAENDKNHLSEKQDTYLSNSSMSNSYS
YHSDEVYNDSGYLSKNKLDSGIEPVLKNVEDQKNTSFSKVISNVKDANAYPQTVNEDICVEELVTSSSPC
KNKNAAIKLSISNSNNFEVGPPAFRIASGKIVCVSHETIKKVKDIFTDSFSKVIKENNENKSKICQTKIM
AGCYEALDDSEDILHNSLDNDECSTHSHKVFADIQSEEILQHNQNMSGLEKVSKISPCDVSLETSDICKC
SIGKLHKSVSSANTCGIFSTASGKSVQVSDASLQNARQVFSEIEDSTKQVFSKVLFKSNEHSDQLTREEN
TAIRTPEHLISQKGFSYNVVNSSAFSGFSTASGKQVSILESSLHKVKGVLEEFDLIRTEHSLHYSPTSRQ
NVSKILPRVDKRNPEHCVNSEMEKTCSKEFKLSNNLNVEGGSSENNHSIKVSPYLSQFQQDKQQLVLGTK
VSLVENIHVLGKEQASPKNVKMEIGKTETFSDVPVKTNIEVCSTYSKDSENYFETEAVEIAKAFMEDDEL
TDSKLPSHATHSLFTCPENEEMVLSNSRIGKRRGEPLILVGEPSIKRNLLNEFDRIIENQEKSLKASKST
PDGTIKDRRLFMHHVSLEPITCVPFRTTKERQEIQNPNFTAPGQEFLSKSHLYEHLTLEKSSSNLAVSGH
PFYQVSATRNEKMRHLITTGRPTKVFVPPFKTKSHFHRVEQCVRNINLEENRQKQNIDGHGSDDSKNKIN
DNEIHQFNKNNSNQAAAVTFTKCEEEPLDLITSLQNARDIQDMRIKKKQRQRVFPQPGSLYLAKTSTLPR
ISLKAAVGGQVPSACSHKQLYTYGVSKHCIKINSKNAESFQFHTEDYFGKESLWTGKGIQLADGGWLIPS
NDGKAGKEEFYRALCDTPGVDPKLISRIWVYNHYRWIIWKLAAMECAFPKEFANRCLSPERVLLQLKYRY
DTEIDRSRRSAIKKIMERDDTAAKTLVLCVSDIISLSANISETSSNKTSSADTQKVAIIELTDGWYAVKA
QLDPPLLAVLKNGRLTVGQKIILHGAELVGSPDACTPLEAPESLMLKISANSTRPARWYTKLGFFPDPRP
FPLPLSSLFSDGGNVGCVDVIIQRAYPIQWMEKTSSGLYIFRNEREEEKEAAKYVEAQQKRLEALFTKIQ
EEFEEHEENTTKPYLPSRALTRQQVRALQDGAELYEAVKNAADPAYLEGYFSEEQLRALNNHRQMLNDKK
QAQIQLEIRKAMESAEQKEQGLSRDVTTVWKLRIVSYSKKEKDSVILSIWRPSSDLYSLLTEGKRYRIYH
LATSKSKSKSERANIQLAATKKTQYQQLPVSDEILFQIYQPREPLHFSKFLDPDFQPSCSEVDLIGFVVS
VVKKTGLAPFVYLSDECYNLLAIKFWIDLNEDIIKPHMLIAASNLQWRPESKSGLLTLFAGDFSVFSASP
KEGHFQETFNKMKNTVENIDILCNEAENKLMHILHANDPKWSTPTKDCTSGPYTAQIIPGTGNKLLMSSP
NCEIYYQSPLSLCMAKRKSVSTPVSAQMTSKSCKGEKEIDDQKNCKKRRALDFLSRLPLPPPVSPICTFV
SPAAQKAFQPPRSCGTKYETPIKKKELNSPQMTPFKKFNEISLLESNSIADEELALINTQALLSGSTGEK
QFISVSESTRTAPTSSEDYLRLKRRCTTSLIKEQESSQASTEECEKNKQDTITTKKYI
----refp_db-----
$ formatdb -i refp_db -p T -o T
----tp53.fa-----
>gi|187233964|gb|ACD01221.1| TP53 [Homo sapiens]
RAMAIYKQSQHMTEVVRRCPTNERCSDSDGLAPPQHLIR
----tp53.fa-----
$ blastall -p blastp -i tp53.fa -d refp_db
Fix broken packages
Probably mixed ubuntu distributions, ie jaunty and intrepid
Check
$ sudo vi /etc/apt/sources.list
and remove jaunty
$ sudo apt-get install autoremove
$ sudo apt-get -f install xine-ui vlc mplayer
$ sudo apt-get build-dep mplayer meconder
Check
$ sudo vi /etc/apt/sources.list
and remove jaunty
$ sudo apt-get install autoremove
$ sudo apt-get -f install xine-ui vlc mplayer
$ sudo apt-get build-dep mplayer meconder
Monday, March 8, 2010
Quick programming reference
C++
http://www.stumbleupon.com/su/3dhSXA/www.sourcepole.com/sources/programming/cpp/cppqref.html
Perl
http://www.doulos.com/knowhow/perl/quick_start/
http://www.stumbleupon.com/su/3dhSXA/www.sourcepole.com/sources/programming/cpp/cppqref.html
Perl
http://www.doulos.com/knowhow/perl/quick_start/
Writing scalable applications
http://msdn.microsoft.com/en-us/library/ms810434.aspx
http://code.google.com/appengine/articles/scaling/overview.html
* Minimizing work - Retrieve objects/entities by key, key name, or ID, Paging results, read / write sparsely
* Paging through large datasets
* Avoiding datastore contention
* Sharding counters
* Effective memcache
http://msdn.microsoft.com/en-us/magazine/cc163854.aspx#S4
Performance on the Data Tier
Tip 1—Return Multiple Resultsets
Tip 2—Paged Data Access
Tip 3—Connection Pooling
Tip 4—ASP.NET Cache API
Tip 5—Per-Request Caching
Tip 6—Background Processing
Tip 7—Page Output Caching and Proxy Servers
Tip 8—Run IIS 6.0 (If Only for Kernel Caching)
Tip 9—Use Gzip Compression
Tip 10—Server Control View State
Conclusion
http://www.javaperformancetuning.com/tips/design.shtml#REF2
J2EE Patterns
MVC http://java.sun.com/blueprints/patterns/MVC-detailed.html
http://java.sun.com/blueprints/patterns/catalog.html
http://code.google.com/appengine/articles/scaling/overview.html
* Minimizing work - Retrieve objects/entities by key, key name, or ID, Paging results, read / write sparsely
* Paging through large datasets
* Avoiding datastore contention
* Sharding counters
* Effective memcache
http://msdn.microsoft.com/en-us/magazine/cc163854.aspx#S4
Performance on the Data Tier
Tip 1—Return Multiple Resultsets
Tip 2—Paged Data Access
Tip 3—Connection Pooling
Tip 4—ASP.NET Cache API
Tip 5—Per-Request Caching
Tip 6—Background Processing
Tip 7—Page Output Caching and Proxy Servers
Tip 8—Run IIS 6.0 (If Only for Kernel Caching)
Tip 9—Use Gzip Compression
Tip 10—Server Control View State
Conclusion
http://www.javaperformancetuning.com/tips/design.shtml#REF2
J2EE Patterns
MVC http://java.sun.com/blueprints/patterns/MVC-detailed.html
http://java.sun.com/blueprints/patterns/catalog.html
Sunday, March 7, 2010
Pokemon Top abilities
http://www.smogon.com/smog/issue4/top_abilities
480 spd-def-a Lopunny normal wk: fighting
525 sa-a Lucario fight/steel wk: fire/fighting/ground
545 sa-sd Togekiss normal/flying wk: rock / elec / ice
480 sa/a Octillery water wk: grass / elec
540 hp-sp.def-sp.a Blissey normal wk: fighting
510 def-a Gliscor ground/flying wk: ice / water
525 a-def Torterra grass/ground
480 spd Froslass ice
525 sp-a Glaceon ice
600 Garchomp dragon/ground wk: dragon/ice, special
500 sp-a Wailord water
425 sp-a chimecho psychic
http://www.youtube.com/watch?v=aFUV6N9ZIys
Battle vs Synthia
http://www.youtube.com/watch?v=S6tBB1ksgLc&feature=fvsr
Types
http://www.smogon.com/dp/types/
HM Slave - Gyrados, Bibarel, Tropius, Skarmory
http://bulbapedia.bulbagarden.net/wiki/Appendix:HM_slave
Where To Find Good Rod In Pokemon Platinum?
U can find the good rod on route 209 east from hearthome city :}
Where do you get a Super Rod on Pokemon Platinum?
Find a fisherman in the Fight Area. You need to have the National Dex. It is at the northeast exit (top left).
POKEMON PLATINUM: HOW TO GET REMORAID?
You need to fish with the Good Rod on Route 212 South, Route 213, Route 222, Route 223, Route 224, Route 230, Pastoria City, Sunyshore City, or at the Pokemon League. It is common and should be easy to catch
Hustle increases the user's Attack stat by 50%, but lowers the Accuracy of the user's Physical moves by 20%. Special moves are unaffected by Hustle.
http://www.smogon.com/dp/pokemon/octillery
Sniper multiplies the base power of an attack 1.5× during a critical hit.
List of Pokemon with Unique Type combinations
http://bulbapedia.bulbagarden.net/wiki/List_of_Pok%C3%A9mon_with_unique_type_combinations
http://bulbapedia.bulbagarden.net/wiki/Happiness
Hidden Power?
However, in Platinum, there is a man in the Veilstone Game Corner Prize Exchange house that will tell the player the type of their Pokémon's Hidden Power. In HeartGold and SoulSilver, he is present in the Celadon Game Corner Prize Exchange house
http://bulbapedia.bulbagarden.net/wiki/Hidden_Power_(move)
Honey (wait 6 1/4 hours)
http://bulbapedia.bulbagarden.net/wiki/Honey
http://wiki.answers.com/Q/What_do_you_have_to_do_when_you_have_put_honey_on_a_tree_on_pokemon_diamond
Soft reset DS
heyy! heres how to SR a DS L + R + Select + Start and .... HOLD!!
Pokemon tips / cheats
http://www.neoseeker.com/Games/cheats/DS/pokemon_platinum.html
Nature
Lonely: +attack, -defense
Brave: +attack, -speed
Adamant: +attack, -special attack
Naughty: +attack, -special defense
Bold: +defense, -attack
Relaxed: +defense, -defense
Impish: +defense, -special attack
Lax: +defense, -special defense
Timid: +speed, -attack
Hasty: +speed, -defense
Jolly: +speed, -special attack
Naive: +speed, -special defense
Modest: +special attack, -attack
Mild: +special attack, -defense
Quiet: +special attack, -speed
Rash: +special attack, -special defense
Calm: +special defense, -attack
Careful: +special defense, -special attack
Gentle: +special defense, -defense
Sassy: +special defense, -speed
Hardy: Neutral
Docile: Neutral
Serious: Neutral
Bashful: Neutral
Quirky: Neutral
obtain trade evolution pokemon
Obtain Trade-Evolution Pokemon
Pokemon such as Graveler, Haunter, Machoke, and Kadabra will only evolve when traded. You can use this trick to evolve these Pokemon using only a single DS.
Requirements:
Must have access to GTS
Must have Wi-Fi
1. Head to the GTS in Jubilife City with the Pokemon you want to evolve.
2. Deposit your Pokemon in the GTS. Request something that is IMPOSSIBLE or very rare to get, to decrease the chances of your Pokemon being traded. If your deposited Pokemon is traded, the trick will fail.
3. Seek for a Pokemon on the GTS and make any trade.
4. Once you finish the trade, withdraw the Pokemon you had deposited in the GTS. If you did the trick right, it should evolve as if it was traded.
You can do this trick with any Pokemon that is evolved through trading.
480 spd-def-a Lopunny normal wk: fighting
525 sa-a Lucario fight/steel wk: fire/fighting/ground
545 sa-sd Togekiss normal/flying wk: rock / elec / ice
480 sa/a Octillery water wk: grass / elec
540 hp-sp.def-sp.a Blissey normal wk: fighting
510 def-a Gliscor ground/flying wk: ice / water
525 a-def Torterra grass/ground
480 spd Froslass ice
525 sp-a Glaceon ice
600 Garchomp dragon/ground wk: dragon/ice, special
500 sp-a Wailord water
425 sp-a chimecho psychic
http://www.youtube.com/watch?v=aFUV6N9ZIys
Battle vs Synthia
http://www.youtube.com/watch?v=S6tBB1ksgLc&feature=fvsr
Types
http://www.smogon.com/dp/types/
HM Slave - Gyrados, Bibarel, Tropius, Skarmory
http://bulbapedia.bulbagarden.net/wiki/Appendix:HM_slave
Where To Find Good Rod In Pokemon Platinum?
U can find the good rod on route 209 east from hearthome city :}
Where do you get a Super Rod on Pokemon Platinum?
Find a fisherman in the Fight Area. You need to have the National Dex. It is at the northeast exit (top left).
POKEMON PLATINUM: HOW TO GET REMORAID?
You need to fish with the Good Rod on Route 212 South, Route 213, Route 222, Route 223, Route 224, Route 230, Pastoria City, Sunyshore City, or at the Pokemon League. It is common and should be easy to catch
Hustle increases the user's Attack stat by 50%, but lowers the Accuracy of the user's Physical moves by 20%. Special moves are unaffected by Hustle.
http://www.smogon.com/dp/pokemon/octillery
Sniper multiplies the base power of an attack 1.5× during a critical hit.
List of Pokemon with Unique Type combinations
http://bulbapedia.bulbagarden.net/wiki/List_of_Pok%C3%A9mon_with_unique_type_combinations
http://bulbapedia.bulbagarden.net/wiki/Happiness
Hidden Power?
However, in Platinum, there is a man in the Veilstone Game Corner Prize Exchange house that will tell the player the type of their Pokémon's Hidden Power. In HeartGold and SoulSilver, he is present in the Celadon Game Corner Prize Exchange house
http://bulbapedia.bulbagarden.net/wiki/Hidden_Power_(move)
Honey (wait 6 1/4 hours)
http://bulbapedia.bulbagarden.net/wiki/Honey
http://wiki.answers.com/Q/What_do_you_have_to_do_when_you_have_put_honey_on_a_tree_on_pokemon_diamond
Soft reset DS
heyy! heres how to SR a DS L + R + Select + Start and .... HOLD!!
Pokemon tips / cheats
http://www.neoseeker.com/Games/cheats/DS/pokemon_platinum.html
Nature
Lonely: +attack, -defense
Brave: +attack, -speed
Adamant: +attack, -special attack
Naughty: +attack, -special defense
Bold: +defense, -attack
Relaxed: +defense, -defense
Impish: +defense, -special attack
Lax: +defense, -special defense
Timid: +speed, -attack
Hasty: +speed, -defense
Jolly: +speed, -special attack
Naive: +speed, -special defense
Modest: +special attack, -attack
Mild: +special attack, -defense
Quiet: +special attack, -speed
Rash: +special attack, -special defense
Calm: +special defense, -attack
Careful: +special defense, -special attack
Gentle: +special defense, -defense
Sassy: +special defense, -speed
Hardy: Neutral
Docile: Neutral
Serious: Neutral
Bashful: Neutral
Quirky: Neutral
obtain trade evolution pokemon
Obtain Trade-Evolution Pokemon
Pokemon such as Graveler, Haunter, Machoke, and Kadabra will only evolve when traded. You can use this trick to evolve these Pokemon using only a single DS.
Requirements:
Must have access to GTS
Must have Wi-Fi
1. Head to the GTS in Jubilife City with the Pokemon you want to evolve.
2. Deposit your Pokemon in the GTS. Request something that is IMPOSSIBLE or very rare to get, to decrease the chances of your Pokemon being traded. If your deposited Pokemon is traded, the trick will fail.
3. Seek for a Pokemon on the GTS and make any trade.
4. Once you finish the trade, withdraw the Pokemon you had deposited in the GTS. If you did the trick right, it should evolve as if it was traded.
You can do this trick with any Pokemon that is evolved through trading.
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