Laboratory Resources

Resources for Gene and Protein Analysis

Boston-area Seminars and Events

• http://biologyweek.wi.mit.edu

Molecular Biology and Protein Structure Resource

http://www.sdsc.edu/pb/edu/pharm207/pharm207.html

Ecoli Summary Sequence View

• http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Protein+Table&list_uids=115

EcoGene: database of Escherichia coli sequence and function

• http://www.ecogene.org

EcoliWiki

• http://ecoliwiki.net

WikiGenes

• http://www.wikigenes.org/

HHPred

• http://protevo.eb.tuebingen.mpg.de/toolkit/index.php?view=hhpred
  (CATH and superfam, plus a selection of others)

Multiple Sequence Alignment

• Probcons http://probcons.stanford.edu/
• Muscle http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.pya
• MAFFT: http://mafft.cbrc.jp/alignment/software/
• http://align.genome.jp/mafft/

UniProt

• http://www.pir.uniprot.org/index.shtml

SMART

• http://smart.embl-heidelberg.de/
• http://www.ebi.ac.uk/InterProScan/
• http://curie.utmb.edu/prosurf.html /
• http://phylogenomics.berkeley.edu/INTREPID/

BIND

• http://www.bind.ca/Action

Genome Sequence Analysis

• http://openhelix.com/index.shtml
• http://genome.ucsc.edu
• http://www.ensembl.org/index.html
• http://www.ensembl.org/info/worked_example.pdf
• more bacteria: http://genome.jgi-psf.org
  

Japanese E. coli stock center

• http://ecoli.aist-nara.ac.jp/GB5/search.jsp

CellProfiler is designed for biologists without training in computer
vision or programming to quantitatively measure phenotypes from
thousands of images automatically.
www.cellprofiler.org

DNA sequencing results analysis

• http://www.geospiza.com/finchtv/download/index.html (Macs and PC)

Science News

• http://www.world-science.net

Environmental Health and Safety

Northeastern EHS: http://www.ehs.neu.edu/

Training Required for all Beuning lab members

• Note: On-line training must be completed using NEU-network computers only.
• Laboratory Safety/Chemical Hygiene Training (on-line)
• Hazardous Waste Training (classroom)
• Radiation Awareness Training (on-line)
• Radiation User Training (on-line and classroom)
• Autoclave Training (on-line and in-person)
• Bloodborne Pathogens and Biosafety (classroom)

• Laboratory Resources
• Lab Tour