Integrated Calendar

UCSC Table browser & Galaxy: asking large scale questions

In this workshop we will cover advanced uses of the UCSC Genome browser: the Table browser and custom tracks. We will also cover basic usage of Galaxy, and the interface between Galaxy and UCSC.
This workshop will start with a lecture and will also have a hands-on session at the end with a prepared exercise, although participants are encouraged to come with their own data/questions.

Prerequisite: Basic knowledge of how to use the UCSC Genome browser. The basics will NOT be covered.

The proton is not "fundamental" in the same way as the point-like electron. In fact, it is a composite system composed of quarks and gluons. When we probe a proton with an electron beam in inclusive scattering, the deviation from simple point-like behavior is characterized by four structure functions, each of which describes a particular aspect of the proton's compositeness. Three of the four structure functions are fairly well determined. The fourth structure function g2^p is relatively unknown and its knowledge is critical for a full understanding of the simplest bound atomic systems, notably, the hydrogen atom, which stimulated the construction of QED. Currently, one of the main uncertainties in understanding these simple bound systems comes from our knowledge of g2^p. We will discuss recent results from the Jlab spin structure program and give a perspective on upcoming experiments.

PARTEK WORKSHOP

Hosted by Dr. Ester Feldmesser,
Bioinformatics Unit, Weizmann Institute of Science

Sponsored by Eisenberg Bros. Ltd.

8th -10th November 2011

Trainers: Drs Jörg Mages & Ivan K. Lukić, European Support Team

*For registration and additional details Please contact*:

Amos Grundwag, Eisenberg Bros. Ltd.

amosg@eisenbros.co.il

*Agenda:*

Tuesday, November 8th , 2011:

*Lecture and Demo:*

Location: Max and Lillian Candiotty Building Seminar Room, Weizmann Institute

*9:00 - 12:00* (Coffee break 10:30)

*Partek Genomics Suite (TM) Overview*

- Partek 101

- Statistics

- Introduction to Gene Expression Microarray Data

*Hands on sessions -- for registered attendees only:*

Location: PC classroom, Room 101 Levine Building, Weizmann Institute

*13:30 - 17:00 *(Coffee break 15:00)

*Gene Expression Analysis of Microarray Data: Hands-on Exercice*

*Wednesday, November 9th , 2011:*

*Hands on sessions -- for registered attendees only:*

Location: PC classroom, Room 101 Levine Building, Weizmann Institute

*Use of Partek Flow and Partek Genomics Suite as a start-to-finish solution in the analysis of next-generation sequencing data including quality control, alignment, mapping, statistics, and visualization options.*

*9:00 - 12:30*(Coffee break 10:30)

*Partek Flow (TM) Demonstration*

. Overview of Partek solutions for NGS

. QA/QC for NGS data

. Alignment

*RNA-Seq Workflow: Hands-on Exercise*

*13:30 - 17:00 *(Coffee break 15:00)

*RNA-Seq Workflow: Hands-on Exercise*

*ChIP-Seq Workflow: Hands-on Exercice*

*Thursday, November 10th , 2011: *

*Hands on sessions -- for registered attendees only:*

*Use of Partek Genomics Suite in the analysis copy number microarray data, integration of copy number workflow with loss of heterozygosity and allele-specific copy number workflows.*

*9:00 - 12:30*(Coffee break 10:30)

*Copy Number Workflow: Hands-on Exercice*

*13:30 - 16:30 *(Coffee break 15:00)

*Open Lab: Bring Your Own Data*

This session is a hands-on open-lab format where participants may bring their own data and go through analysis with the guidance of the Partek customer support team. We recommend to discuss data formats and particularly the annotation files in advance with our trainers. Please feel free to contact them directly:

Jörg Mages jmages@partek.com

Ivan Lukić ilukic@partek.com




*9:00 -- 12:30*(Coffee break 10:30)

*Partek? Flow^(TM) Demonstration*

. Overview of Partek solutions for NGS

. QA/QC for NGS data

. Alignment

*RNA-Seq Workflow: Hands-on Exercise*

*13:30 -- 17:00 *(Coffee break 15:00)

*RNA-Seq Workflow: Hands-on Exercise*

*ChIP-Seq Workflow: Hands-on Exercice*

*Thursday, November 10^th , 2011: *

*Hands on sessions -- for registered attendees only:*

*Use of Partek Genomics Suite in the analysis copy number microarray data, integration of copy number workflow with loss of heterozygosity and allele-specific copy number workflows.*

*9:00 -- 12:30*(Coffee break 10:30)

*Copy Number Workflow: Hands-on Exercice*

*13:30 -- 16:30 *(Coffee break 15:00)

*Open Lab: Bring Your Own Data*

This session is a hands-on open-lab format where participants may bring their own data and go through analysis with the guidance of the Partek customer support team. We recommend to discuss data formats and particularly the annotation files in advance with our trainers.

Repetitive transcranial magnetic stimulation (rTMS) has been shown to induce neurophysiological changes in the cortex that can be recorded through electroencephalography. Oscillatory activity in the gamma (30-50 Hz) frequency range represents a neurophysiological process that has been shown to be altered during working memory, a cognitive process that is mediated by the dorsolateral prefrontal cortex (DLPFC). We examined the effect of 20 Hz rTMS applied bilaterally to the DLPFC on gamma oscillations elicited during the N-back working memory task in 22 healthy subjects and 24 patients with schizophrenia. Patients with SCZ then continued to receive rTMS (active or sham) for an additional 4 weeks (i.e., 20 treatments in total). Compared to sham rTMS, active rTMS produced a significant increase in gamma oscillations in healthy subjects that was most pronounced in the 3-back condition, the condition associated with greatest cognitive demand. In patients with schizophrenia, by contrast, active rTMS reduced gamma oscillations compared to sham. Neither group demonstrated significant changes in other frequency ranges, suggesting that rTMS selectively modulates only gamma oscillations. In addition, after an additional 4 weeks of active rTMS evidence suggests a potentiation of N-back performance compared to sham but no significant changes in negative symptoms. These findings suggest that patients with schizophrenia demonstrate altered gamma modulation which may be normalized in response to rTMS and over time translate into improved cognitive performance. These findings may also provide important insights into the mechanisms that lead to enhanced cognitive performance.

Colloidal core/shell heterostructures with alloy composition: Synthesis, theoretical electronic band structure, and magneto-optical characterization
Prof. Efrat Lifshitz, Schulich Faculty of Chemistry, Russell Berrie Nanotechnology Institute, Solid State Institute, Technion, Haifa, 32000, Israel
Two decades of research were devoted to explore the electronic properties of semiconductor nanocyrstals by varying their size, shape and surface coverage. The option to engineer the properties is of a significant importance for the materials’ implementation as absorbers or emitters in photovoltaic cells, light emitting diodes, optical switches, gain devices, photodetectors, thermoelectric, spintronics devices and biological platforms. However, some of these applications impose constrains on the size and shape, say, incorporating them into biological membrane or a mesoporous substrate, while retaining the demand for a suitable emission color. These restrictions can be overcome by new strategies gaining property control using: (a) alloyed ternary or quaternary compounds, when a ternary material is comprised of two different cations/anions with a common anion/cation, while quaternary includes four elements. In all, the elements can be either distributed homogeneously or exhibit a graded composition along a selective direction; (b) core/shell heterostructures, comprised of a semiconductor core (sphere or rod shape), covered by a shell, of another semiconductor, when the band-edge off-set at the core/shell interface, can be tuned from a type-I (when shell ban-edge is rapping that of the core), through qausi-type-II, to a type-II (when, band-edge of the constituents are staggered) alignment. Moreover, one of the constituents (core or shell) may have alloyed composition.
The present work demonstrates a progressive effort in the synthesis of alloyed colloidal quantum dots (QDs) or nanorods (NRs), by employing an effective high-temperature synthetic strategy with balancing of precursors’ reactivity. Unique alloyed core/shell heterostructures, such as PbSe/PbSexS1-x,1 CdTe/CdTexSe1-x, and CdSe/CdSexS1-x/CdS,2 were developed, offering better crystallographic and dielectric match at the dot/shell or rod/shell interface, regulating carriers’ delocalization and/or charge separation by tunability of the band off-set. Theoretical description of the electronic band structure of alloyed core, dot/shell or a rod/shell nanocrystals, using a k*p model, covered a wide physical aspects, including an effective mass anisotropy, dielectric variation between the constituents, a sharp or a smooth off-set at the core/shell interface and electron-hole Coulomb interactions, laid a ground for tailoring heterostructures with the desired composition and optical properties. Representative theoretical plot of a charge distribution between a dot and a shell in a QD is shown in Fig. 1.4 Engineering of a band-edge, as well as the remote energy states of alloyed PbSexS1-x QD is illustrated in Fig. 2. This figure reveals a few interesting aspects, related to grouping of states nearly into min-bands with a degeneracy that depends on composition (x) and even some level crossing. The physical explanation will be discussed in the talk.4
Experimental evidences investigating the mentioned heterostructures showed a relatively high emission quantum yield, chemical stability, and in a few cases (e.g., CdTe/CdTexSe1-x/CdSe) an option to stabilize an emission intensity, pronounced as a blinking free behavior when measuring a single QD.2 Further on, significant knowledge on carriers’ localization was gained by the use of a magneto-optical methodology, e.g., optically detected magnetic resonance (ODMR) spectroscopy, supplying a magnetic resonance identification of a carrier and its surrounding, phenomenological g-factor, electron-hole exchange interaction and crystal anisotropy.3

1. (a) Brumer M., et al., Adv. Funct. Mater., 2005, 15, 1111; (b) Maikov G., et al., ACSNano, 2010, 4, 6547.
2. (a) Osovsky R., et al. Phys. Rev. Lett. 2009, 102, 197401, (b) Wang F. et al. Nature 2009, 459, 686-689.
3. (a) Lifshitz E., et al., Annual Review of Physical Chemistry, 2004, 55, 509; (b) unpublished results.
4. R. Vaxenburg, E. Lifshitz, submitted (2011)