GersteinInfo - User contributions [en]

Resources

2017-12-04T21:35:58Z

Lucasl: /* Functional Annotation */

The tools & resources listed below have been '''published and are actively maintained''' by the Gerstein lab. You may view a list of the associated literature [http://papers.gersteinlab.org/subject/coretools/index.html '''here'''].

In addition to the tools below, the lab has also published a number of [http://info.gersteinlab.org/More_tools '''tools that are not currently being actively maintained'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

Source code for all software is available on our [http://github.gersteinlab.org/ Github page].

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://molmovdb.mbb.yale.edu/molmovdb/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Networks===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 10px;"
|style="width:15%; text-align:center;"| [[File:Network.jpg|center|x75px]] [http://networks.gersteinlab.org/ Networks] ||
The Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments. To this end, we have developed a portal for our network research.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

===Structural Variants (SV)===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:SVpage logo.png‎|center|x85px]] [http://sv.gersteinlab.org/ Structural Variants]||
Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).
|}

=Data Sets=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style="width:7%; text-align:center;"|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
|}

=Evolution=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style="width:7%; text-align:center;"|2008||An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including statistical coupling analysis (SCA), explicit likelihood of subset variation (ELSC), mutual information and correlation-based methods.
|}

=Genome Technology=

===Gene Regulation===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/Loregic '''Loregic''']||style="width:7%; text-align:center;"|2015||Loregic is a computational method integrating gene expression and regulatory network data, to characterize the logical cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target, and finds the gate that best matches each triplet’s observed gene expression pattern across many conditions. Using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs.
|}

===Allele-Specific Effects===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleledb.gersteinlab.org '''AlleleDB''']||style="width:7%; text-align:center;"|2016||AlleleDB is an online resource for storing and visualizing allele-specific binding (ASB) and gene expression (ASE). Using variants from the 1000-Genomes Project and RNA-seq and ChIP-seq data from related projects, this resource serves as a repository for the catalog of ASB and ASE variants, associated genomic elements and personal genomes used in the study. AlleleDB also interfaces with the UCSC browser for visualization of results.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style="width:7%; text-align:center;"|2011||AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then maps RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations in which there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified, thereby providing evidence for allele-specific events.
|}

===ChIP-Seq ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://music.gersteinlab.org '''MUSIC'''] [http://github.gersteinlab.org/MUSIC/ Github repo] ||style="width:7%; text-align:center;"|2014||
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style="width:7%; text-align:center;"|2009|| A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as input DNA. PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances.
|}

===Functional Annotation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq'''] - & - [http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style="width:7%; text-align:center;"|2013 & 2014||These tools can be used to automatically score and annotate the disease-causing potential of SNVs, particularly those which are non-coding. FunSeq can detect recurrent annotation elements in non-coding regions when running with multiple personal genomes. FunSeq2 is an extension of FunSeq that provides a means of prioritizing somatic variants from cancer whole genome sequencing.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://larva.gersteinlab.org/ '''LARVA'''] [https://github.com/gersteinlab/LARVA Github repo] ||style="width:7%; text-align:center;"|2015||LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features (such as replication timing) to better estimate local mutation rates and mutational enrichments.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT'''] [http://github.gersteinlab.org/vat/ Github repo] ||style="width:7%; text-align:center;"|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://aloft.gersteinlab.org/ '''ALoFT'''] [https://github.com/gersteinlab/aloft Github repo] ||style="width:7%; text-align:center;"|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://moat.gersteinlab.org/ '''MOAT'''] [https://github.com/gersteinlab/MOAT Github repo] ||style="width:7%; text-align:center;"|2017|| MOAT (Mutations Overburdening Annotations Tool) is a computational system for identifying significant mutation burdens in genomic elements with an empirical, nonparametric method. Taking a set of variant calls and a set of annotations, MOAT calculates which annotations have observed variant counts that are substantially elevated with respect to a distribution of expected variant counts determined by permutation of the input data.
|}

===Microarrays & Proteomics===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''MOTIPS''']||style="width:7%; text-align:center;"|2010||MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|2007||Protein Abundance and mRNA Expression (PARE) is a tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which may warrant further investigation.
|}

===RNA-Seq===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://act.gersteinlab.org/ '''ACT''']||style="width:7%; text-align:center;"|2011||The aggregation and correlation toolbox (ACT) is an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq'''] [http://github.gersteinlab.org/FusionSeq/ Github repo]||style="width:7%; text-align:center;"|2010||FusionSeq may be used to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also includes a module to identify exact sequences at breakpoint junctions.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq'''] [http://github.gersteinlab.org/IQSeq/ Github repo]||style="text-align:center;"|2012||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools'''] [http://github.gersteinlab.org/RSEQtools/ Github repo]||style="text-align:center;"|2011||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF is a compact data format that enables anonymization of confidential sequence information while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
|}

=== Structural Variation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE'''] [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style="width:7%; text-align:center;"|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] [http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style="width:7%; text-align:center;"|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.
|}

=Networks=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style="width:7%; text-align:center;"|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style="width:7%; text-align:center;"|2014||A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://pubnet.gersteinlab.org/ '''PubNet''']||style="width:7%; text-align:center;"|2005||A web-based tool that extracts several types of relationships returned by PubMed queries and maps them on to networks, allowing for graphical visualization, textual navigation, and topological analysis.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style="width:7%; text-align:center;"|2004||TopNet is an automated web tool designed compare the topologies of sub-networks, looking for global differences associated with different types of proteins. This automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein network.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|2006||(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.
|}

=Structure and Macromolecular Motions=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [http://3vee.molmovdb.org/ '''3V''']||style="width:7%; text-align:center;"|2010||
The 3V web server extracts and comprehensively analyzes the internal volumes of input RNA and protein structures. It identifies internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|2006||The Helix Interaction Tool (HIT) is a comprehensive package for analyzing helix-helix packing in proteins. This enables the user to obtain quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style="width:7%; text-align:center;"|1994-2009||A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution. Included is a library functions for analyzing structures, a convenient interactive command-line interpreter, and software for the calculation of geometrical quantities associated with macromolecular structures and their motions.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style="width:7%; text-align:center;"|2000||A web server for generating and viewing models of protein conformational change using interpolation with energy minimization. The user may opt to use either single- or multi-chain proteins as input.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://stress.molmovdb.org/ '''STRESS'''] [https://github.com/gersteinlab/STRESS Github repo] ||style="width:7%; text-align:center;"|2016||STRucturally-identified ESSential residues (STRESS) is a web tool that enables users to submit PDB-formatted protein structures to predict both surface- and interior-allosteric residues. The software behind this tool employs 3D structures to build models of protein conformational change in order to perform allosteric site predictions.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://intensification.gersteinlab.org// '''Intensification'''] [https://github.com/gersteinlab/Intensification Github repo] ||style="width:7%; text-align:center;"|2016||Intensification is a database that contains the results for 12 repeat protein domains, from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). We make use of the modular structure of repeat motifs to amplify signals of selection from population genetics and traditional inter-species conservation.
|-style="height: 100px;"
|}

=more=
[http://info.gersteinlab.org/More_tools more tools & resources]

Resources

2017-12-04T21:25:49Z

Lucasl: /* Functional Annotation */

The tools & resources listed below have been '''published and are actively maintained''' by the Gerstein lab. You may view a list of the associated literature [http://papers.gersteinlab.org/subject/coretools/index.html '''here'''].

In addition to the tools below, the lab has also published a number of [http://info.gersteinlab.org/More_tools '''tools that are not currently being actively maintained'''].

You may also access tools that have [http://info.gersteinlab.org/Even_more_tools '''not yet been published''']

Source code for all software is available on our [http://github.gersteinlab.org/ Github page].

=Portals=

=== MolMovDB ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:Morph-icon.jpg‎]] [http://molmovdb.mbb.yale.edu/molmovdb/ MolMovDB] ||
Servers and a suite of accessory tools for the analysis of conformational changes in protein and nucleic acid structures.
|}

===Networks===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 10px;"
|style="width:15%; text-align:center;"| [[File:Network.jpg|center|x75px]] [http://networks.gersteinlab.org/ Networks] ||
The Gerstein lab has been a pioneer in applying network analysis to generate knowledge form large-scale experiments. To this end, we have developed a portal for our network research.
|}

===Pseudogene.org===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:pseudogene.png‎]] [http://www.pseudogene.org/ Pseudogene.org] ||Pseudogene.org is a collection of resources related to our efforts to survey eukaryotic genomes for pseudogene sequences, "pseudo-fold" usage, amino-acid composition, and single-nucleotide polymorphisms (SNPs) to help elucidate the relationships between pseudogene families across several organisms.
|}

===Structural Variants (SV)===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [[File:SVpage logo.png‎|center|x85px]] [http://sv.gersteinlab.org/ Structural Variants]||
Software that may be used to investigate Structural Variations (SVs) and Copy Number Variations (CNVs).
|}

=Data Sets=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/breakdb/ '''BreakDB''']||style="width:7%; text-align:center;"|2009||This database, which is part of the PEMer package, contains information about structural variants and associated breakpoints.
|}

=Evolution=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://coevolution.gersteinlab.org/coevolution/ '''Coevolution analysis of protein residues''']||style="width:7%; text-align:center;"|2008||An integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including statistical coupling analysis (SCA), explicit likelihood of subset variation (ELSC), mutual information and correlation-based methods.
|}

=Genome Technology=

===Gene Regulation===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/Loregic '''Loregic''']||style="width:7%; text-align:center;"|2015||Loregic is a computational method integrating gene expression and regulatory network data, to characterize the logical cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target, and finds the gate that best matches each triplet’s observed gene expression pattern across many conditions. Using human ENCODE ChIP-Seq and TCGA RNA-Seq data, we are able to demonstrate how Loregic characterizes complex circuits involving both proximally and distally regulating transcription factors (TFs) and also miRNAs.
|}

===Allele-Specific Effects===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleledb.gersteinlab.org '''AlleleDB''']||style="width:7%; text-align:center;"|2016||AlleleDB is an online resource for storing and visualizing allele-specific binding (ASB) and gene expression (ASE). Using variants from the 1000-Genomes Project and RNA-seq and ChIP-seq data from related projects, this resource serves as a repository for the catalog of ASB and ASE variants, associated genomic elements and personal genomes used in the study. AlleleDB also interfaces with the UCSC browser for visualization of results.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://alleleseq.gersteinlab.org/home.html '''AlleleSeq''']||style="width:7%; text-align:center;"|2011||AlleleSeq is a computational pipeline that is used to study allele-specific expression (ASE) and allele specific binding (ASB). The pipeline first constructs a diploid personal genome sequence, then maps RNA-seq and ChIP-seq functional genomic data onto this personal genome. Consequently, locations in which there are differences in number of mapped reads between maternally- and paternally-derived sequences can be identified, thereby providing evidence for allele-specific events.
|}

===ChIP-Seq ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://music.gersteinlab.org '''MUSIC'''] [http://github.gersteinlab.org/MUSIC/ Github repo] ||style="width:7%; text-align:center;"|2014||
MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/PeakSeq/ '''PeakSeq'''] [http://github.gersteinlab.org/PeakSeq/ Github repo] ||style="width:7%; text-align:center;"|2009|| A tool for calling peaks corresponding to transcription factor binding sites from ChIP-Seq data scored against a matched control such as input DNA. PeakSeq employs a two-pass strategy in which putative binding sites are first identified in order to compensate for genomic variation in the 'mappability' of sequences, before a second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances.
|}

===Functional Annotation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://funseq.gersteinlab.org/ '''FunSeq'''] - & - [http://funseq2.gersteinlab.org/ '''FunSeq2'''] [http://github.gersteinlab.org/FunSeq2/ Github] ||style="width:7%; text-align:center;"|2013 & 2014||These tools can be used to automatically score and annotate the disease-causing potential of SNVs, particularly those which are non-coding. FunSeq can detect recurrent annotation elements in non-coding regions when running with multiple personal genomes. FunSeq2 is an extension of FunSeq that provides a means of prioritizing somatic variants from cancer whole genome sequencing.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://larva.gersteinlab.org/ '''LARVA'''] [https://github.com/gersteinlab/LARVA Github repo] ||style="width:7%; text-align:center;"|2015||LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features (such as replication timing) to better estimate local mutation rates and mutational enrichments.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://vat.gersteinlab.org/ '''VAT'''] [http://github.gersteinlab.org/vat/ Github repo] ||style="width:7%; text-align:center;"|2012|| A computational framework to functionally annotate variants in personal genomes using a cloud-computing environment.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://aloft.gersteinlab.org/ '''ALoFT'''] [http://github.gersteinlab.org/aloft/ Github repo] ||style="width:7%; text-align:center;"|2017|| A method to annotate and predict the disease-causing potential of loss-of-function variants.
|-style="height: 100px;"

|style="width:15%; text-align:center;"|[http://moat.gersteinlab.org/ '''MOAT'''] [http://github.gersteinlab.org/MOAT/ Github repo] ||style="width:7%; text-align:center;"|2017|| MOAT (Mutations Overburdening Annotations Tool) is a computational system for identifying significant mutation burdens in genomic elements with an empirical, nonparametric method. Taking a set of variant calls and a set of annotations, MOAT calculates which annotations have observed variant counts that are substantially elevated with respect to a distribution of expected variant counts determined by permutation of the input data.
|}

===Microarrays & Proteomics===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://motips.gersteinlab.org/ '''MOTIPS''']||style="width:7%; text-align:center;"|2010||MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|2007||Protein Abundance and mRNA Expression (PARE) is a tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which may warrant further investigation.
|}

===RNA-Seq===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://act.gersteinlab.org/ '''ACT''']||style="width:7%; text-align:center;"|2011||The aggregation and correlation toolbox (ACT) is an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/rnaseq/fusionseq/ '''FusionSeq'''] [http://github.gersteinlab.org/FusionSeq/ Github repo]||style="width:7%; text-align:center;"|2010||FusionSeq may be used to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also includes a module to identify exact sequences at breakpoint junctions.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq'''] [http://github.gersteinlab.org/IQSeq/ Github repo]||style="text-align:center;"|2012||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
|-style="height: 100px;"
|style="text-align: center;"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools'''] [http://github.gersteinlab.org/RSEQtools/ Github repo]||style="text-align:center;"|2011||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF is a compact data format that enables anonymization of confidential sequence information while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
|}

=== Structural Variation ===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/age/ '''AGE'''] [http://papers.gersteinlab.org/papers/age/index.html (citation)]||style="width:7%; text-align:center;"|2011|| AGE is used for defining breakpoints of genomic structural variants at single-nucleotide resolution, using optimal alignments with gap excision.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://sv.gersteinlab.org/cnvnator/ '''CNVnator'''] [http://papers.gersteinlab.org/papers/CNVnator/index.html (citation)]||style="width:7%; text-align:center;"|2011|| CNVnator may be used to discover, genotype, and characterize typical and atypical CNVs from familial and population genome sequencing.
|}

=Networks=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://archive.gersteinlab.org/proj/DynaSIN/index.html '''DynaSIN''']||style="width:7%; text-align:center;"|2011||The Dynamic Structure Interaction Network (DynaSIN) is a resource for studying protein-protein interaction networks in the context of conformational changes.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[https://github.com/gersteinlab/OrthoClust '''OrthoClust''']||style="width:7%; text-align:center;"|2014||A computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://pubnet.gersteinlab.org/ '''PubNet''']||style="width:7%; text-align:center;"|2005||A web-based tool that extracts several types of relationships returned by PubMed queries and maps them on to networks, allowing for graphical visualization, textual navigation, and topological analysis.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/core.html '''TopNet''']||style="width:7%; text-align:center;"|2004||TopNet is an automated web tool designed compare the topologies of sub-networks, looking for global differences associated with different types of proteins. This automated web tool designed to address this question, calculating and comparing topological characteristics for different sub-networks derived from any given protein network.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|2006||(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.
|}

=Structure and Macromolecular Motions=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
!Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|style="width:15%; text-align:center;"| [http://3vee.molmovdb.org/ '''3V''']||style="width:7%; text-align:center;"|2010||
The 3V web server extracts and comprehensively analyzes the internal volumes of input RNA and protein structures. It identifies internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://helix.gersteinlab.org/ '''HIT''']||style="width:7%; text-align:center;"|2006||The Helix Interaction Tool (HIT) is a comprehensive package for analyzing helix-helix packing in proteins. This enables the user to obtain quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://geometry.molmovdb.org '''Macromolecular Geometry and Packing Tools''']||style="width:7%; text-align:center;"|1994-2009||A number of programs for calculating properties of protein and nucleic acid structures have been collected into a single distribution. Included is a library functions for analyzing structures, a convenient interactive command-line interpreter, and software for the calculation of geometrical quantities associated with macromolecular structures and their motions.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://www2.molmovdb.org/wiki/info/index.php/Morph_Server '''Morph Server''']||style="width:7%; text-align:center;"|2000||A web server for generating and viewing models of protein conformational change using interpolation with energy minimization. The user may opt to use either single- or multi-chain proteins as input.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://stress.molmovdb.org/ '''STRESS'''] [https://github.com/gersteinlab/STRESS Github repo] ||style="width:7%; text-align:center;"|2016||STRucturally-identified ESSential residues (STRESS) is a web tool that enables users to submit PDB-formatted protein structures to predict both surface- and interior-allosteric residues. The software behind this tool employs 3D structures to build models of protein conformational change in order to perform allosteric site predictions.
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://intensification.gersteinlab.org// '''Intensification'''] [https://github.com/gersteinlab/Intensification Github repo] ||style="width:7%; text-align:center;"|2016||Intensification is a database that contains the results for 12 repeat protein domains, from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). We make use of the modular structure of repeat motifs to amplify signals of selection from population genetics and traditional inter-species conservation.
|-style="height: 100px;"
|}

=more=
[http://info.gersteinlab.org/More_tools more tools & resources]

Main Page

2017-06-26T14:49:31Z

Lucasl: /* Important Public Items */

== Important Public Items ==
*[[Selected Press Accounts Highlighting Gerstein Lab Work| '''Press Accounts''']] highlighting the lab
*'''[[FAQ]]''' on tools and data
*Lab '''[[Calendar]]'''
*Info. on [[Homepage image gallery | '''Homepage Images''']] (including [http://www.gersteinlab.org/media/images gallery of all images] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions Permissions] on using material generated by the lab
*Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]])
*A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.com GLMinutes.wordpress.com] (more info about the [[Wordpress Minutes Stream]])

__TOC__

In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*Misc. Public [[Documents]] about the lab
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== More Info for New People ==
* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for new people starting in the lab from the private wiki
* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
**[[Lab Dropbox]]
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [http://hpc.yale.edu/ls-account-request/ Yale High Performance Computing Center]

* Calls, meetings, &c
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&on=downloads Other info])

* Some Useful University Policies
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]

Main Page

2017-06-25T22:01:14Z

Lucasl: /* Important Public Items */

== Important Public Items ==
*[[Selected Press Accounts Highlighting Gerstein Lab Work| '''Press Accounts''']] highlighting the lab
*'''[[FAQ]]''' on tools and data
*Lab '''[[Calendar]]'''
*Info. on [[Homepage image gallery | '''Homepage Images''']] (including [http://www.gersteinlab.org/media/images gallery of all images] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions Permissions] on using material generated by the lab
*Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]])
*A (password-protected) archive of the lab's minutes thread is available at [http://glminutes.wordpress.org GLMinutes.wordpress.org] (more info about the [[Wordpress Minutes Stream]])

__TOC__

In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*Misc. Public [[Documents]] about the lab
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== More Info for New People ==
* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for new people starting in the lab from the private wiki
* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
**[[Lab Dropbox]]
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [http://hpc.yale.edu/ls-account-request/ Yale High Performance Computing Center]

* Calls, meetings, &c
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&on=downloads Other info])

* Some Useful University Policies
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]

Wordpress Minutes Stream

2017-06-25T22:00:31Z

Lucasl: Created page with 'The Wordpress Minutes Stream is a new experiment to organize the lab's minutes with the help of Wordpress. The idea is to use tags to cluster the items on the minutes thread for …'

The Wordpress Minutes Stream is a new experiment to organize the lab's minutes with the help of Wordpress. The idea is to use tags to cluster the items on the minutes thread for easier future retrieval.

The Minutes Stream can be accessed on Wordpress.com at:

[http://glminutes.wordpress.com/ glminutes.wordpress.com]

There is also a fully mirrored version here, which also includes tag cloud pages for quickly retrieving minutes with a certain tag:

[http://glminutes.gersteinlab.org/ glminutes.gersteinlab.org]

Any emails sent to [mailto:minutes@gersteinlab.org minutes@gersteinlab.org] will appear on both sites.

Both pages are marked private, and require login to access. For both sites, the standard user account for non-admin access is "glreader" (password shared to the "all" list)

Currently, the tags we're using are:

*summary
*scheduling
*todo

In the future, we may use tags for specific meetings and projects.

Main Page

2017-06-25T21:47:46Z

Lucasl: /* Important Public Items */

== Important Public Items ==
*[[Selected Press Accounts Highlighting Gerstein Lab Work| '''Press Accounts''']] highlighting the lab
*'''[[FAQ]]''' on tools and data
*Lab '''[[Calendar]]'''
*Info. on [[Homepage image gallery | '''Homepage Images''']] (including [http://www.gersteinlab.org/media/images gallery of all images] & [http://www.gersteinlab.org/index.html.1jun11 old version] of homepage )
*[https://sites.gersteinlab.org/permissions Permissions] on using material generated by the lab
*Public posts of links and useful info to the lab are at [http://linkstream.gersteinlab.org LinkStream.gersteinlab.org] (more info. about the [[Linkstream]])
*An archive of the lab's minutes thread is available at [http://glminutes.wordpress.org GLMinutes.wordpress.org] (password protected)

__TOC__

In general, this wiki hosts general, public information about the [http://gersteinlab.org '''Gerstein Lab'''], beyond that on the homepage. Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "public"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

<HR>

== Other Stuff for the Public ==
*Info on [[Bioinformatics Lab Information System (BLIS)]] (utilizing Google Docs API)
*[[Summaries]] of lab research
*Misc. Public [[Documents]] about the lab
*[[Status of Lab Web Resources]]
*Vectorized Yale logo, download [http://archive.gersteinlab.org/docs/2015/05.19/Yale_logo.eps here]

== More Info for New People ==
* [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab Information] for new people starting in the lab from the private wiki
* [http://wiki.gersteinlab.org/labinfo/Staff People] to look for to get oriented
* About [http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure Group Meetings and JClubs]

== Info for Lab Members and Collaborators ==
* Working on drafts, papers, grants, presentations &c
** Lab [[Resources Document]] (NIH form)
**[[Lab Dropbox]]
** Conventions for editing Google Docs - http://goo.gl/kSrS9
** Pointers on [[Streamlining Draft Flow]] (Ideas related to the process of drafting and submitting papers)
** [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
** [[CRAMTOOLS and common directory]]

* Computing
** [http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
** [http://hpc.yale.edu/ls-account-request/ Yale High Performance Computing Center]

* Calls, meetings, &c
**[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
**[http://wiki.gersteinlab.org/labinfo/Subscribing_NIH_email_list Subscribing to a NIH email list] page.
** Information on [[Meeting Invites]]
** [https://portal.infocus.com/support/Product%20Downloads/InFocus_IN3114_3116_ReferenceGuide_EN.pdf Manual] for new projector ([https://portal.infocus.com/support/Product%20Pages/downloads.aspx?mic=IN3116&on=downloads Other info])

* Some Useful University Policies
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]

* Misc
**[[Getting Mark's signature for documents]]
**[[Temperature in Bass 432a]], real time measurements (see how cold it gets)
**Prominent [[public wiki pages linked from elsewhere]]
**[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
**[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
**[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
** [[Recommendation Letters]]
**[https://docs.google.com/spreadsheet/pub?key=0ApmN6KUB6ILdcDh0Z1luZ3VnTVc3QV9YSmtQaXBpZXc&single=true&gid=2&output=html Magazine Subscriptions]
** Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
** Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]

Calendar maintainers

2017-05-11T20:21:56Z

Lucasl:

The individuals below have responsibilities for maintaining different parts of the lab calendar. These should *also* try to turn up on their call.

<pre>
- Wormfly -------- JX (gcal)
- sv2anal -------- FN,XK (gcal)
- Entex ---------- JR,TG
- Psychencode ---- SL
- Gencode -------- PM
- gsp/cmg -------- AH,BW
- encode4 -------- JZ
- exrna ---------- JR
- ncvarg --------- SKL
- 1000G-SV ------- FN,XK
- pcawg ---------- SK
- special events - JR
</pre>

2011-06-07T18:37:47Z

Lucasl:

This wiki hosts general, public information about the

'''[http://gersteinlab.org Gerstein Lab]'''.

Lab members should consult the [http://wiki.gersteinlab.org/labinfo/ private lab wiki] for lab-specific information (login as user "public"). There's also a wiki for [http://wiki.gersteinlab.org/meetings lab meetings] (login as user "private"). To edit this wiki, contact the [[User:Infoadmin | Infoadmin]]

== Important Public Items ==
*Public [[Documents]] about the lab
*[[FAQ]] (new) on programs
*Lab [[Calendar]]
*[http://www.gersteinlab.org/index.html.1jun11 Old version] of lab homepage
*Prominent [[public wiki pages linked from elsewhere]]
*[[Permissions]]

== Info for New People ==
*[[General Information for New Undergraduates]] thinking about working in the lab
* Information for new people starting in the lab from the private wiki ([http://wiki.gersteinlab.org/labinfo/Group_Meeting_and_JC_Procedure], [http://wiki.gersteinlab.org/labinfo/Bad_Times_and_Contact_Info], [http://wiki.gersteinlab.org/labinfo/New_People_Entering_Lab], [http://wiki.gersteinlab.org/labinfo/Staff])

== Info for Lab Members and Collaborators ==
*[http://wiki.gersteinlab.org/labinfo/Lab_Computing_Resources Lab Computing Resources] page.
*[http://wiki.gersteinlab.org/labinfo/Making_conference_calls_or_lab_related_calls Making phone calls] (SKYPE information included) page.
*[http://wiki.gersteinlab.org/labinfo/Using_copier Using copier] page.
*[http://www.facebook.com/group.php?gid=54856837624 Gerstein Lab Facebook Page]
*[http://bioinfo.mbb.yale.edu/pipermail/web/ Public WEB Mailing List] (no longer in use)
* [[Streamlining Draft Flow]] (Ideas for streamlining the process of drafting and submitting papers)
** Way to list Mark's [[Affiliation]] on papers
** See [[xxmg at gersteinlab.org | xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
** Note that '''xxmg at bioinfo.mbb.yale.edu''' for paper correspondence is deprecated.
* [[Pointers on Powerpoints]] and [[Pointers on Grant Sections]]
* [[Recommendation Letters]]
* Lab [[Resources Document]] (NIH form)
* Google Groups: [http://group.gersteinlab.org homepage], for [http://docs.google.com/a/gersteinlab.org DOCS]
* Some Useful University Policies
** Snippets from [[MB&B Policy for Graduate Students on Vacation and Travel]] and [[Policy on Postdoc Appointments]]
** Policies on visitors: [http://provost.yale.edu/minors-in-labs Policy on Minors in Labs] ([http://archive.gersteinlab.org/docs/2010/06.02/Policy-on-Minors-in-Labs.pdf old]), [http://provost.yale.edu/policy-access-university-labs-and-research-facilities Policy on Access to the Lab]
** Travel per diem information: [http://www.yale.edu/ppdev/Guides/bluepages.pdf Yale Blue Pages]
* Useful links: [http://www.yale.edu/its/accounts/netid.html Yale NetID System], [http://www.yale.edu/its/network/vpn_faq.html Yale VPN FAQ], [http://www.yale.edu/its/network/wireless/faq.html Yale Wireless FAQ], [http://www.yale.edu/its/telecom/dialing.html Yale Dialing Instructions], [https://config.mail.yale.edu Configuring Yale email], [http://www.yale.edu/ris/main.html Poster Printing]
* [http://maguro.cs.yale.edu:8000/Center_for_High_Performance_Computation_in_Biology_and_Biomedicine Yale High Performance Computing Center]
* Information on [[what grant to charge something to]]
* Information on [[Meeting Invites]]
* [http://araman.mbgnet/nagios/ System Status] MBGNet LAN access only.
* [http://info.gersteinlab.org/Tools Tools] page