The document describes a workshop on variant calling and bioinformatics tools for genetic variant annotation. It discusses converting between DNA, mRNA and protein variants, using tools like Mutalyzer, SeattleSeq and Provean/SIFT to annotate variants for functional impact. It also covers searching ExAC for allele frequencies and ClinVar for reports in other patients. The workshop teaches using criteria to classify variants as pathogenic, likely pathogenic, uncertain significance or benign.
The document summarizes the activities of the IBP Data Management team from October 2014. It discusses the migration of several crop databases to the new IBDB v2 system, including maize, sorghum, cassava, beans, chickpeas, groundnuts, rice, wheat, and poplar data. It also covers the documentation of additional crop traits, establishment of databases for new crops like lentils and soybeans, and development of a data import tool to load historical datasets. Finally, it discusses the reorganization of database scripts to standardize data handling across crops.
The document discusses various databases and resources for analyzing proteins and chemical compounds. It describes the Conserved Domain Database, which contains models of conserved protein domains and alignments. It also mentions CD tree, which allows viewing conserved domains. Other resources discussed include protein clusters, which group related protein sequences, and biosystems, which describe interacting biological components like genes and proteins. The document also provides information about PubChem, including the Compound, Substance, and BioAssay databases that contain chemical structures, sample descriptions, and biological screening results.
The National Center for Biotechnology Information (NCBI) was created in 1988 as part of the National Library of Medicine at NIH. It establishes public databases for biological research, develops software tools for sequence analysis, and disseminates biomedical information from its location in Bethesda, MD. NCBI houses several integrated databases including PubMed, GenBank, RefSeq, and UniGene that contain literature, sequences, gene information, and more.
What is Creativity made of? Where do ideas come from, and how can you get more of them? How can you make them better? What happens when there is no box to think outside of? Jason Theodor, a long-standing Creative Director in the digital advertising world, has asked himself these questions for years. These are his observations from the field, and his tools for ideation.
This presentation breaks down the creative method and explores the fundamental elements of creativity. It describes multiple systems for idea generation, problem solving, and originality. It emphasizes the importance of routines, explains appropriate brainstorming techniques, and much more: all with unexpected examples and takeaways.
If you want to live a more creative life, or give yourself an edge in the Age of Ideas, this presentation is a must see.
The document describes a workshop on variant calling and bioinformatics tools for genetic variant annotation. It discusses converting between DNA, mRNA and protein variants, using tools like Mutalyzer, SeattleSeq and Provean/SIFT to annotate variants for functional impact. It also covers searching ExAC for allele frequencies and ClinVar for reports in other patients. The workshop teaches using criteria to classify variants as pathogenic, likely pathogenic, uncertain significance or benign.
The document summarizes the activities of the IBP Data Management team from October 2014. It discusses the migration of several crop databases to the new IBDB v2 system, including maize, sorghum, cassava, beans, chickpeas, groundnuts, rice, wheat, and poplar data. It also covers the documentation of additional crop traits, establishment of databases for new crops like lentils and soybeans, and development of a data import tool to load historical datasets. Finally, it discusses the reorganization of database scripts to standardize data handling across crops.
The document discusses various databases and resources for analyzing proteins and chemical compounds. It describes the Conserved Domain Database, which contains models of conserved protein domains and alignments. It also mentions CD tree, which allows viewing conserved domains. Other resources discussed include protein clusters, which group related protein sequences, and biosystems, which describe interacting biological components like genes and proteins. The document also provides information about PubChem, including the Compound, Substance, and BioAssay databases that contain chemical structures, sample descriptions, and biological screening results.
The National Center for Biotechnology Information (NCBI) was created in 1988 as part of the National Library of Medicine at NIH. It establishes public databases for biological research, develops software tools for sequence analysis, and disseminates biomedical information from its location in Bethesda, MD. NCBI houses several integrated databases including PubMed, GenBank, RefSeq, and UniGene that contain literature, sequences, gene information, and more.
What is Creativity made of? Where do ideas come from, and how can you get more of them? How can you make them better? What happens when there is no box to think outside of? Jason Theodor, a long-standing Creative Director in the digital advertising world, has asked himself these questions for years. These are his observations from the field, and his tools for ideation.
This presentation breaks down the creative method and explores the fundamental elements of creativity. It describes multiple systems for idea generation, problem solving, and originality. It emphasizes the importance of routines, explains appropriate brainstorming techniques, and much more: all with unexpected examples and takeaways.
If you want to live a more creative life, or give yourself an edge in the Age of Ideas, this presentation is a must see.
2. Springer exemplar
〜学術論文中の特定の単語やフレーズが、どのような文脈・用法で使用されているのか?を検索
h:p://www.springerexemplar.com
Springer’s
collec)on
to
find
authen)c
examples
of
how
a
word
or
phrase
is
used
in
published
literature.
2
興味のある研究がどの雑誌に掲載され
ているか?を調べることができる
論文を投稿する際にも参考になる
どこの国で、その分野の研究が盛んで
あるか?を知ることが出来る
Pubmed検索でヒットしない文献も
調べることが可能
論文を執筆する際にも使える
3.
phytozome 10
〜植物ゲノムDB
h:p://phytozome.jgi.doe.gov/pz/portal.html
Sta)s)cs
Genome
Size
726,616,606
base
pairs
arranged
in
2n=20
chromosomes
Loci
33,032
loci
containing
protein-‐coding
transcripts
Transcripts
39,441
protein-‐coding
transcripts
3
様々な植物のゲノム情報を収集できる
4.
phytozome 10
〜植物ゲノムDB
h:p://phytozome.jgi.doe.gov/pz/portal.html
植物ゲノム情報をダウンロード可能
fa
-‐>
fasta
file
annota)on
file
protein
gene
cds
gff3
-‐>
Generic
Feature
Format
version
3
4
6.
TogoTV
〜生命科学分野の有用なデータベースやツールの使い方を動画で紹介
h:ps://www.youtube.com/user/togotv
Tutorial
videos
of
bioinforma2cs
resources:
online
distribu2on
trial
in
Japan
named
TogoTV
6